PDB Short entry for 2C7M HEADER PROTEIN BINDING 25-NOV-05 2C7M TITLE HUMAN RABEX-5 RESIDUES 1-74 IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74; COMPND 5 SYNONYM: RABEX-5, GEF 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN; COMPND 9 CHAIN: B 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 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 9 ORGANISM_COMMON: BOVINE; SOURCE 10 ORGANISM_TAXID: 9913; SOURCE 11 OTHER_DETAILS: BOSTON BIOCHEM KEYWDS PROTEIN-BINDING, UBIQUITIN COMPLEX, UBIQUITIN BINDING DOMAIN, KEYWDS 2 ENDOCYTOSIS, NUCLEAR PROTEIN, POLYPROTEIN, UBL CONJUGATION, PROTEIN KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.PENENGO,M.MAPELLI,A.G.MURACHELLI,S.CONFALIONERI,L.MAGRI, AUTHOR 2 A.MUSACCHIO,P.P.DI FIORE,S.POLO,T.R.SCHNEIDER REVDAT 6 08-MAY-19 2C7M 1 REMARK REVDAT 5 13-JUN-18 2C7M 1 TITLE JRNL REMARK REVDAT 4 24-FEB-09 2C7M 1 VERSN REVDAT 3 29-MAR-06 2C7M 1 JRNL REVDAT 2 01-MAR-06 2C7M 1 AUTHOR JRNL REVDAT 1 15-FEB-06 2C7M 0 JRNL AUTH L.PENENGO,M.MAPELLI,A.G.MURACHELLI,S.CONFALONIERI,L.MAGRI, JRNL AUTH 2 A.MUSACCHIO,P.P.DI FIORE,S.POLO,T.R.SCHNEIDER JRNL TITL CRYSTAL STRUCTURE OF THE UBIQUITIN BINDING DOMAINS OF JRNL TITL 2 RABEX-5 REVEALS TWO MODES OF INTERACTION WITH UBIQUITIN. JRNL REF CELL V. 124 1183 2006 JRNL REFN ISSN 0092-8674 JRNL PMID 16499958 JRNL DOI 10.1016/J.CELL.2006.02.020 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7655 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 392 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 417 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.64000 REMARK 3 B22 (A**2) : -4.64000 REMARK 3 B33 (A**2) : 6.95000 REMARK 3 B12 (A**2) : -2.32000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.262 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.866 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1088 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1462 ; 2.380 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 129 ; 6.924 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;35.947 ;25.179 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 212 ;19.987 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;24.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 821 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 398 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 720 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 39 ; 0.167 ; 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): 33 ; 0.169 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.089 ; 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): 683 ; 1.306 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1046 ; 2.068 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 483 ; 3.979 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 416 ; 6.065 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 : B 1 B 73 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0590 14.3470 18.0530 REMARK 3 T TENSOR REMARK 3 T11: -0.2579 T22: -0.1325 REMARK 3 T33: -0.1985 T12: 0.0039 REMARK 3 T13: -0.0941 T23: -0.0645 REMARK 3 L TENSOR REMARK 3 L11: 11.5810 L22: 5.5790 REMARK 3 L33: 6.0194 L12: 0.3270 REMARK 3 L13: -1.8505 L23: 2.3088 REMARK 3 S TENSOR REMARK 3 S11: -0.1043 S12: -0.8194 S13: 0.6825 REMARK 3 S21: 0.5793 S22: 0.0637 S23: -0.3693 REMARK 3 S31: 0.0125 S32: 0.4354 S33: 0.0407 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 : A 18 A 39 REMARK 3 ORIGIN FOR THE GROUP (A): 40.0410 11.3680 10.0760 REMARK 3 T TENSOR REMARK 3 T11: -0.2148 T22: 0.2136 REMARK 3 T33: 0.2582 T12: -0.0317 REMARK 3 T13: -0.0873 T23: -0.1450 REMARK 3 L TENSOR REMARK 3 L11: 21.5103 L22: 3.3604 REMARK 3 L33: 9.2796 L12: -0.4141 REMARK 3 L13: 6.0266 L23: -1.6423 REMARK 3 S TENSOR REMARK 3 S11: -0.2477 S12: 1.0629 S13: 0.6526 REMARK 3 S21: -0.4938 S22: 0.1376 S23: -0.7555 REMARK 3 S31: 0.0292 S32: 1.0855 S33: 0.1101 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 40 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): 66.3220 6.1470 26.9930 REMARK 3 T TENSOR REMARK 3 T11: -0.1399 T22: -0.2962 REMARK 3 T33: -0.2530 T12: -0.0287 REMARK 3 T13: 0.0653 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 52.4317 L22: 2.1364 REMARK 3 L33: 18.3496 L12: -3.6484 REMARK 3 L13: 25.4856 L23: -1.7316 REMARK 3 S TENSOR REMARK 3 S11: 0.7266 S12: -0.0299 S13: -1.0441 REMARK 3 S21: -0.0002 S22: -0.2880 S23: 0.1608 REMARK 3 S31: 0.3688 S32: 0.2154 S33: -0.4386 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2C7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8066 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 18.50 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 43.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL2MAP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROP 300 NL PLUS 300 NL 20 REMARK 280 MG/ML PROTEIN SOLUTION 0.2 M LIS2SO4, 0.1 MES PH 6.5 25% PEG3350, REMARK 280 PH 6.50, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.36667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.73333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.55000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 45.91667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.18333 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 300 REMARK: THE QUATERNARY STRUCTURE FOR THIS ENTRY IS REMARK 300 NOT RELEVANTSINCE THE COMPLEX IS ONLY MADE UP OF REMARK 300 FRAGMENTS OF RABEX-5IN COMPLEX WITH UBIQUITIN. REMARK 300 HOWEVER, THESE REMARKSONLY INDICATE THE COMPLEX AS REMARK 300 SEEN IN THE PDB FILE, ANDDO NOT HAVE RELEVANCE REMARK 300 TO THE BIOLOGICAL STATE OF THEMOLECULE. 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 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 MET A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 ARG A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 ILE A 11 REMARK 465 HIS A 12 REMARK 465 VAL A 13 REMARK 465 ASP A 14 REMARK 465 GLN A 15 REMARK 465 SER A 16 REMARK 465 ASP A 17 REMARK 465 GLY B 75 REMARK 465 GLY B 76 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 74 CA C O CB CG CD NE REMARK 470 ARG B 74 CZ NH1 NH2 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 O HOH B 2016 O HOH B 2017 2.12 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 GLU A 65 CG GLU A 65 CD 0.092 REMARK 500 GLU B 16 CD GLU B 16 OE1 0.076 REMARK 500 GLU B 16 CD GLU B 16 OE2 0.070 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 LEU A 18 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 ARG A 48 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 LEU A 62 CB - CG - CD2 ANGL. DEV. = -14.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 20 131.20 -39.84 REMARK 500 PRO B 38 -35.34 -39.08 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 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 CYS A 24 SG 129.6 REMARK 620 3 CYS A 36 SG 112.2 93.1 REMARK 620 4 CYS A 39 SG 114.6 100.0 102.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAR RELATED DB: PDB REMARK 900 DI-UBIQUITIN REMARK 900 RELATED ID: 1E0Q RELATED DB: PDB REMARK 900 MUTANT PEPTIDE FROM THE FIRST N-TERMINAL 17 AMINO-ACID OF UBIQUITIN REMARK 900 RELATED ID: 1P3Q RELATED DB: PDB REMARK 900 MECHANISM OF UBIQUITIN RECOGNITION BY THE CUE DOMAIN OF VPS9 REMARK 900 RELATED ID: 1UZX RELATED DB: PDB REMARK 900 A COMPLEX OF THE VPS23 UEV WITH UBIQUITIN REMARK 900 RELATED ID: 1V80 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR REMARK 900 RELATED ID: 1V81 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR REMARK 900 RELATED ID: 1WR6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GGA3 GAT DOMAIN IN COMPLEX WITHUBIQUITIN REMARK 900 RELATED ID: 1WRD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TOM1 GAT DOMAIN IN COMPLEX WITHUBIQUITIN REMARK 900 RELATED ID: 1YD8 RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN REMARK 900 RELATED ID: 2BGF RELATED DB: PDB REMARK 900 NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT REMARK 900 PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA REMARK 900 RELATED ID: 2C7N RELATED DB: PDB REMARK 900 HUMAN RABEX-5 RESIDUES 1-74 IN COMPLEX WITH UBIQUITIN DBREF 2C7M A 2 75 UNP Q53FG0 Q53FG0_HUMAN 1 74 DBREF 2C7M B 1 76 UNP P62990 UBIQ_BOVIN 1 76 SEQRES 1 A 74 MET SER LEU LYS SER GLU ARG ARG GLY ILE HIS VAL ASP SEQRES 2 A 74 GLN SER ASP LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR SEQRES 3 A 74 GLY ASN PRO ALA TRP GLN GLY PHE CYS SER LYS CYS TRP SEQRES 4 A 74 ARG GLU GLU TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN SEQRES 5 A 74 GLU ASP TRP GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU SEQRES 6 A 74 GLU GLU ALA PHE ALA SER SER GLN SER 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 ZN A 500 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *37(H2 O) HELIX 1 1 ASN A 29 GLN A 33 5 5 HELIX 2 2 CYS A 36 SER A 75 1 40 HELIX 3 3 THR B 22 GLY B 35 1 14 HELIX 4 4 PRO B 37 ASP B 39 5 3 HELIX 5 5 LEU B 56 ASN B 60 5 5 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 ZN ZN A 500 SG CYS A 20 1555 1555 2.25 LINK ZN ZN A 500 SG CYS A 24 1555 1555 2.65 LINK ZN ZN A 500 SG CYS A 36 1555 1555 2.54 LINK ZN ZN A 500 SG CYS A 39 1555 1555 2.29 SITE 1 AC1 4 CYS A 20 CYS A 24 CYS A 36 CYS A 39 CRYST1 81.900 81.900 55.100 90.00 90.00 120.00 P 61 6 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 0.012210 0.007049 0.000000 0.00000 SCALE2 0.000000 0.014099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018149 0.00000