PDB Short entry for 2JF5 HEADER SIGNALING PROTEIN 26-JAN-07 2JF5 TITLE CRYSTAL STRUCTURE OF LYS63-LINKED DI-UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DI-UBIQUITIN, LYS63-LINKED; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ISO-PEPTIDE LINK BETWEEN A-LYS63 AND B-GLY76 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS LYS6, LYS63, NF-KB, UBIQUITIN, NUCLEAR PROTEIN, SIGNAL TRANSDUCTION, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.KOMANDER,P.ODENWAELDER,D.BARFORD REVDAT 5 13-JUL-11 2JF5 1 VERSN REVDAT 4 02-JUN-09 2JF5 1 JRNL REVDAT 3 28-APR-09 2JF5 1 JRNL REVDAT 2 24-FEB-09 2JF5 1 VERSN REVDAT 1 05-FEB-08 2JF5 0 JRNL AUTH D.KOMANDER,F.REYES-TURCU,J.D.F.LICCHESI,P.ODENWAELDER, JRNL AUTH 2 K.D.WILKINSON,D.BARFORD JRNL TITL MOLECULAR DISCRIMINATION OF STRUCTURALLY EQUIVALENT LYS JRNL TITL 2 63-LINKED AND LINEAR POLYUBIQUITIN CHAINS. JRNL REF EMBO REP. V. 10 466 2009 JRNL REFN ISSN 1469-221X JRNL PMID 19373254 JRNL DOI 10.1038/EMBOR.2009.55 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 756 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1014 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.283 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1240 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1671 ; 1.513 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 157 ; 6.116 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;36.390 ;25.439 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 258 ;17.114 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 198 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 897 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 471 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 807 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 76 ; 0.232 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.207 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.191 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 789 ; 0.887 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1243 ; 1.432 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 492 ; 2.226 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 424 ; 3.713 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): 63.7127 81.3647 32.5458 REMARK 3 T TENSOR REMARK 3 T11: -0.2522 T22: -0.2524 REMARK 3 T33: -0.1952 T12: -0.0928 REMARK 3 T13: 0.0305 T23: -0.0305 REMARK 3 L TENSOR REMARK 3 L11: 6.1560 L22: 8.1923 REMARK 3 L33: 2.6521 L12: 2.4955 REMARK 3 L13: 2.2819 L23: 0.4569 REMARK 3 S TENSOR REMARK 3 S11: 0.1544 S12: -0.0981 S13: -0.6355 REMARK 3 S21: -0.3481 S22: 0.1542 S23: -0.5479 REMARK 3 S31: 0.1225 S32: -0.0570 S33: -0.3087 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): 92.3340 105.8642 43.9216 REMARK 3 T TENSOR REMARK 3 T11: -0.2492 T22: -0.2303 REMARK 3 T33: -0.2334 T12: -0.0389 REMARK 3 T13: -0.0918 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 6.8428 L22: 4.4467 REMARK 3 L33: 4.2658 L12: -0.0214 REMARK 3 L13: 0.8271 L23: -0.3700 REMARK 3 S TENSOR REMARK 3 S11: -0.0068 S12: -0.1890 S13: -0.1400 REMARK 3 S21: -0.3220 S22: 0.1050 S23: 0.3767 REMARK 3 S31: 0.1703 S32: -0.3784 S33: -0.0982 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS.DISORDERED RESIDUES HAVE BEEN REFINED WITH REMARK 3 OCCU 0.01. GLY76 IN MOLA IS NOT MODELLED AN ISOPEPTIDE LINKAGE REMARK 3 BETWEEN LYS63 (MOLA) AND GLY76 CONNECTS THE TWO UBIQUITIN REMARK 3 MOIETIES REMARK 4 REMARK 4 2JF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-07. REMARK 100 THE PDBE ID CODE IS EBI-31241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15023 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.95 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.8 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.3 REMARK 200 R MERGE FOR SHELL (I) : 0.59 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1UBQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12 % (W/V) PEG 3350, 5 MM REMARK 280 NICKEL CHLORIDE, 5 MM COBALT CHLORIDE, 5 MM CADMIUM REMARK 280 CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES [PH 7.5] REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.51050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.51050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.51050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.51050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 52.51050 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 52.51050 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 52.51050 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 52.51050 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 52.51050 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 52.51050 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 52.51050 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 52.51050 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 52.51050 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 26.25525 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 78.76575 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 26.25525 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 26.25525 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 26.25525 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 78.76575 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 26.25525 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 78.76575 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 26.25525 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 78.76575 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 26.25525 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 78.76575 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 78.76575 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 26.25525 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 78.76575 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 26.25525 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 26.25525 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 26.25525 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 78.76575 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 26.25525 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 26.25525 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 78.76575 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 78.76575 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 78.76575 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 26.25525 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 78.76575 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 26.25525 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 78.76575 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 26.25525 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 26.25525 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 26.25525 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2006 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 76 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 63 C GLY B 76 1.29 REMARK 500 OE2 GLU B 64 O HOH B 2039 1.92 REMARK 500 O HOH B 2008 O HOH B 2028 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY B 76 C GLY B 76 O 0.159 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1076 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 GLU A 18 OE2 130.1 REMARK 620 3 GLU A 18 OE2 101.4 117.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1076 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 ASP A 21 OD1 83.1 REMARK 620 3 ASP A 21 OD2 130.7 53.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1077 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 29 NZ REMARK 620 2 GLU B 18 OE1 114.9 REMARK 620 3 GLU B 18 OE2 75.3 49.5 REMARK 620 4 ASP B 21 OD1 126.9 93.9 95.5 REMARK 620 5 ASP B 21 OD2 91.3 146.4 126.8 52.6 REMARK 620 6 CL B1080 CL 73.4 110.9 126.6 137.8 96.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1077 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 18 OE1 REMARK 620 2 GLU B 18 OE1 124.9 REMARK 620 3 ASP B 21 OD1 121.4 102.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B1079 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 1 N REMARK 620 2 GLU B 16 OE2 90.5 REMARK 620 3 ASP B 32 OD2 90.8 93.3 REMARK 620 4 HOH B2047 O 110.6 140.7 118.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B1081 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 64 OE1 REMARK 620 2 HIS B 68 NE2 97.7 REMARK 620 3 HOH B2039 O 68.3 63.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1078 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 16 OE2 REMARK 620 2 HOH A2005 O 100.2 REMARK 620 3 MET A 1 N 93.5 121.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A1076 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B1079 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1080 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1078 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B1081 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C3T RELATED DB: PDB REMARK 900 ROTAMER STRAIN AS A DETERMINANT OF PROTEIN REMARK 900 STRUCTURALSPECIFICITY REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 1F9J RELATED DB: PDB REMARK 900 STRUCTURE OF A NEW CRYSTAL FORM OF REMARK 900 TETRAUBIQUITIN REMARK 900 RELATED ID: 1FXT RELATED DB: PDB REMARK 900 STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN REMARK 900 THIOLESTERCOMPLEX REMARK 900 RELATED ID: 1G6J RELATED DB: PDB REMARK 900 STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN REMARK 900 AOT REVERSEMICELLES REMARK 900 RELATED ID: 1GJZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A DIMERIC N-TERMINAL REMARK 900 FRAGMENT OF HUMAN UBIQUITIN REMARK 900 RELATED ID: 1NBF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A UBP-FAMILY REMARK 900 DEUBIQUITINATING ENZYMEIN ISOLATION AND IN REMARK 900 COMPLEX WITH UBIQUITIN ALDEHYDE REMARK 900 RELATED ID: 1OGW RELATED DB: PDB REMARK 900 SYNTHETIC UBIQUITIN WITH FLUORO-LEU AT 50 REMARK 900 AND 67 REMARK 900 RELATED ID: 1Q5W RELATED DB: PDB REMARK 900 UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS REMARK 900 RELATED ID: 1S1Q RELATED DB: PDB REMARK 900 TSG101(UEV) DOMAIN IN COMPLEX WITH UBIQUITIN REMARK 900 RELATED ID: 1SIF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MULTIPLE HYDROPHOBIC REMARK 900 CORE MUTANT OFUBIQUITIN REMARK 900 RELATED ID: 1TBE RELATED DB: PDB REMARK 900 TETRAUBIQUITIN REMARK 900 RELATED ID: 1UBI RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1XD3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UCHL3-UBVME COMPLEX REMARK 900 RELATED ID: 1XQQ RELATED DB: PDB REMARK 900 SIMULTANEOUS DETERMINATION OF PROTEIN STRUCTURE REMARK 900 AND DYNAMICS REMARK 900 RELATED ID: 1YX5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-1/UBIQUITIN REMARK 900 COMPLEX REMARK 900 RELATED ID: 1YX6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-2/UBIQUITIN REMARK 900 COMPLEX REMARK 900 RELATED ID: 1ZGU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE HUMAN MMS2- REMARK 900 UBIQUITIN COMPLEX REMARK 900 RELATED ID: 2AYO RELATED DB: PDB REMARK 900 STRUCTURE OF USP14 BOUND TO UBQUITIN REMARK 900 ALDEHYDE REMARK 900 RELATED ID: 2BGF RELATED DB: PDB REMARK 900 NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN REMARK 900 USING CHEMICAL SHIFT PERTURBATION DATA REMARK 900 TOGETHER WITH RDCS AND 15N-RELAXATION DATA REMARK 900 RELATED ID: 2FCM RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY REMARK 900 SYNTHESIZED [D-GLN35]UBIQUITIN WITH A CUBIC REMARK 900 SPACE GROUP REMARK 900 RELATED ID: 2FCN RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY REMARK 900 SYNTHESIZED [D-VAL35]UBIQUITIN WITH A CUBIC REMARK 900 SPACE GROUP REMARK 900 RELATED ID: 2FCQ RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY REMARK 900 SYNTHESIZEDUBIQUITIN WITH A CUBIC SPACE GROUP REMARK 900 RELATED ID: 2FCS RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY REMARK 900 SYNTHESIZED [L-GLN35]UBIQUITIN WITH A CUBIC REMARK 900 SPACE GROUP REMARK 900 RELATED ID: 2FUH RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE UBCH5C/UB NON- REMARK 900 COVALENT COMPLEX REMARK 900 RELATED ID: 2G45 RELATED DB: PDB REMARK 900 CO-CRYSTAL STRUCTURE OF ZNF UBP DOMAIN REMARK 900 FROM THEDEUBIQUITINATING ENZYME ISOPEPTIDASE T REMARK 900 (ISOT) IN COMPLEXWITH UBIQUITIN REMARK 900 RELATED ID: 2GBK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 9-10 MOAD REMARK 900 INSERTION MUTANT OFUBIQUITIN REMARK 900 RELATED ID: 2GBM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE REMARK 900 INSERTION MUTANTOF UBIQUITIN REMARK 900 RELATED ID: 2GBN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE REMARK 900 INSERTION MUTANTOF UBIQUITIN REMARK 900 RELATED ID: 2J7Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UBIQUITIN-SPECIFIC REMARK 900 PROTEASE ENCODED BY MURINE CYTOMEGALOVIRUS REMARK 900 TEGUMENT PROTEIN M48 IN COMPLEX WITH A REMARK 900 UBQUITIN-BASED SUICIDE SUBSTRATE DBREF 2JF5 A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2JF5 B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET CD B1077 2 HET CD A1076 2 HET CO B1079 1 HET CL B1080 1 HET MG A1078 1 HET CO B1081 1 HETNAM CD CADMIUM ION HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 CD 2(CD 2+) FORMUL 5 CO 2(CO 2+) FORMUL 6 CL CL 1- FORMUL 7 HOH *78(H2 O) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 THR B 22 GLY B 35 1 14 HELIX 5 5 PRO B 37 ASP B 39 5 3 HELIX 6 6 LEU B 56 ASN B 60 5 5 SHEET 1 AA 5 THR A 12 GLU A 16 0 SHEET 2 AA 5 GLN A 2 LYS A 6 -1 O ILE A 3 N LEU A 15 SHEET 3 AA 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA 5 GLN A 41 PHE A 45 -1 O ARG A 42 N VAL A 70 SHEET 5 AA 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 BA 5 THR B 12 GLU B 16 0 SHEET 2 BA 5 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK CD A CD A1076 OD1 ASP A 21 1555 1555 2.17 LINK CD A CD A1076 OE2 GLU A 18 1555 1555 2.10 LINK CD A CD A1076 OE2 GLU A 18 1555 12664 2.60 LINK CD B CD A1076 OE1 GLU A 18 1555 12664 2.40 LINK CD B CD A1076 OD1 ASP A 21 1555 1555 2.17 LINK CD B CD A1076 OD2 ASP A 21 1555 1555 2.64 LINK MG MG A1078 OE2 GLU A 16 1555 1555 2.07 LINK MG MG A1078 O HOH A2005 1555 1555 1.88 LINK MG MG A1078 N MET A 1 1555 1555 1.71 LINK CD A CD B1077 OD1 ASP B 21 1555 1555 2.34 LINK CD A CD B1077 OD2 ASP B 21 1555 1555 2.57 LINK CD A CD B1077 CL CL B1080 1555 1555 2.71 LINK CD B CD B1077 OE1 GLU B 18 1555 1555 2.34 LINK CD B CD B1077 OE1 GLU B 18 1555 10756 2.50 LINK CD B CD B1077 OD1 ASP B 21 1555 1555 2.39 LINK CD A CD B1077 NZ LYS B 29 1555 1555 2.88 LINK CD A CD B1077 OE2 GLU B 18 1555 10756 2.23 LINK CD A CD B1077 OE1 GLU B 18 1555 10756 2.85 LINK CO CO B1079 O HOH B2047 1555 1555 2.33 LINK CO CO B1079 OD2 ASP B 32 1555 7674 2.26 LINK CO CO B1079 OE2 GLU B 16 1555 1555 2.36 LINK CO CO B1079 N MET B 1 1555 1555 1.86 LINK CO CO B1081 O HOH B2039 1555 1555 1.98 LINK CO CO B1081 NE2 HIS B 68 1555 24676 2.27 LINK CO CO B1081 OE1 GLU B 64 1555 1555 2.42 SITE 1 AC1 4 GLU B 18 ASP B 21 LYS B 29 CL B1080 SITE 1 AC2 3 GLU A 18 ASP A 21 LYS A 29 SITE 1 AC3 4 MET B 1 GLU B 16 ASP B 32 HOH B2047 SITE 1 AC4 3 GLU B 18 LYS B 29 CD B1077 SITE 1 AC5 4 MET A 1 GLU A 16 ASP A 32 HOH A2005 SITE 1 AC6 4 GLU B 64 HIS B 68 HOH B2039 HOH B2043 CRYST1 105.021 105.021 105.021 90.00 90.00 90.00 P 43 3 2 48 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009522 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009522 0.00000