PDB Short entry for 2IY1 HEADER HYDROLASE/NUCLEAR PROTEIN 11-JUL-06 2IY1 TITLE SENP1 (MUTANT) FULL LENGTH SUMO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT, RESIDUES 419-643; COMPND 5 SYNONYM: SENP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP1; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 11 CHAIN: B, D; COMPND 12 SYNONYM: SUMO-1, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3 HOMOLOG 3, COMPND 13 UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE PROTEIN UBL1, COMPND 14 GAP-MODIFYING PROTEIN 1, GMP1, SENTRIN, SUMO1; COMPND 15 ENGINEERED: YES 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: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE-NUCLEAR PROTEIN COMPLEX, NUCLEAR PROTEIN, UBL CONJUGATION KEYWDS 2 PATHWAY, PROTEASE, HYDROLASE, UBIQUITIN, THIOL PROTEASE, PROTEIN KEYWDS 3 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.SHEN,C.DONG,J.H.NAISMITH REVDAT 5 28-JUN-17 2IY1 1 REMARK REVDAT 4 13-JUL-11 2IY1 1 VERSN REVDAT 3 24-FEB-09 2IY1 1 VERSN REVDAT 2 20-DEC-06 2IY1 1 JRNL REVDAT 1 15-AUG-06 2IY1 0 JRNL AUTH L.SHEN,M.H.TATHAM,C.DONG,A.ZAGORSKA,J.H.NAISMITH,R.T.HAY JRNL TITL SUMO PROTEASE SENP1 INDUCES ISOMERIZATION OF THE SCISSILE JRNL TITL 2 PEPTIDE BOND. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 1069 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 17099698 JRNL DOI 10.1038/NSMB1172 REMARK 2 REMARK 2 RESOLUTION. 2.46 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 34278 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) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1810 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) : 2.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2412 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 113 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) : 59.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : 0.79000 REMARK 3 B33 (A**2) : -1.57000 REMARK 3 B12 (A**2) : 0.00000 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): 0.394 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.248 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.898 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5234 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7032 ; 1.468 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 614 ; 6.405 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 266 ;40.129 ;24.511 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1018 ;18.205 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.078 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 750 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3918 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2294 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3553 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 216 ; 0.152 ; 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): 56 ; 0.310 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.195 ; 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): 3171 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4990 ; 0.960 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2342 ; 1.522 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2042 ; 2.373 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 421 A 642 1 REMARK 3 1 C 421 C 642 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1853 ; 0.07 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 1853 ; 0.13 ; 0.50 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 17 B 94 1 REMARK 3 1 D 17 D 94 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 B (A): 631 ; 0.07 ; 0.05 REMARK 3 TIGHT THERMAL 2 B (A**2): 631 ; 0.10 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 419 A 644 REMARK 3 ORIGIN FOR THE GROUP (A): 53.7290 44.2750 30.6680 REMARK 3 T TENSOR REMARK 3 T11: -0.2608 T22: -0.1945 REMARK 3 T33: -0.0831 T12: -0.0870 REMARK 3 T13: 0.0510 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 2.7208 L22: 2.3335 REMARK 3 L33: 3.9222 L12: -0.2507 REMARK 3 L13: 0.5847 L23: -0.0418 REMARK 3 S TENSOR REMARK 3 S11: -0.1071 S12: -0.0549 S13: -0.2845 REMARK 3 S21: 0.0145 S22: -0.0275 S23: -0.0048 REMARK 3 S31: -0.0812 S32: 0.1878 S33: 0.1346 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 15 B 96 REMARK 3 ORIGIN FOR THE GROUP (A): 67.4100 38.2900 12.4290 REMARK 3 T TENSOR REMARK 3 T11: -0.1995 T22: 0.0996 REMARK 3 T33: 0.1507 T12: -0.0615 REMARK 3 T13: 0.0605 T23: -0.0645 REMARK 3 L TENSOR REMARK 3 L11: 3.7780 L22: 1.6055 REMARK 3 L33: 7.5617 L12: -0.1356 REMARK 3 L13: -2.3101 L23: 0.7899 REMARK 3 S TENSOR REMARK 3 S11: -0.2461 S12: 0.5796 S13: -0.5172 REMARK 3 S21: -0.3586 S22: 0.0178 S23: -0.1357 REMARK 3 S31: 0.0971 S32: 0.0225 S33: 0.2284 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 : C 419 C 644 REMARK 3 ORIGIN FOR THE GROUP (A): 121.3070 113.5080 29.9230 REMARK 3 T TENSOR REMARK 3 T11: -0.2575 T22: -0.2332 REMARK 3 T33: -0.1401 T12: -0.0060 REMARK 3 T13: 0.0212 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 2.9554 L22: 2.2506 REMARK 3 L33: 2.9924 L12: -0.6829 REMARK 3 L13: 0.5809 L23: -0.1554 REMARK 3 S TENSOR REMARK 3 S11: 0.0483 S12: -0.0828 S13: -0.3536 REMARK 3 S21: -0.0331 S22: -0.0626 S23: 0.0572 REMARK 3 S31: 0.1619 S32: 0.0868 S33: 0.0143 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 15 D 96 REMARK 3 ORIGIN FOR THE GROUP (A): 135.3350 110.8670 11.1980 REMARK 3 T TENSOR REMARK 3 T11: -0.2121 T22: 0.0706 REMARK 3 T33: 0.0694 T12: 0.1046 REMARK 3 T13: 0.0526 T23: -0.0527 REMARK 3 L TENSOR REMARK 3 L11: 2.4065 L22: 2.0683 REMARK 3 L33: 17.8971 L12: 0.2227 REMARK 3 L13: -0.4373 L23: 2.5224 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: 0.4841 S13: -0.2283 REMARK 3 S21: -0.1927 S22: 0.0752 S23: -0.3758 REMARK 3 S31: -0.1793 S32: 0.9601 S33: -0.0423 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2IY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1290029365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34278 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.48200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 70.61600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 70.61600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.22300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 70.61600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 70.61600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.74100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 70.61600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.61600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.22300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 70.61600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.61600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.74100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.48200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: C, D 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 602 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, CYS 602 TO ALA 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 C 570 CD GLU C 570 OE2 -0.068 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 GLU A 570 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 GLU C 570 OE1 - CD - OE2 ANGL. DEV. = -8.7 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 PHE A 420 77.19 -116.42 REMARK 500 ASN A 439 105.74 -49.23 REMARK 500 HIS A 462 -118.77 44.59 REMARK 500 LEU A 530 58.08 -118.05 REMARK 500 SER A 551 2.77 -68.23 REMARK 500 SER B 26 -5.73 82.54 REMARK 500 VAL B 96 -55.20 -10.88 REMARK 500 PHE C 420 78.61 -151.65 REMARK 500 ASN C 437 149.47 -38.81 REMARK 500 ASN C 439 107.98 -49.71 REMARK 500 ARG C 449 39.08 39.30 REMARK 500 HIS C 462 -117.54 36.95 REMARK 500 TYR D 16 -66.22 -135.32 REMARK 500 SER D 26 -6.09 87.45 REMARK 500 GLU D 79 139.32 -36.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CKG RELATED DB: PDB REMARK 900 THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL REMARK 900 BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX REMARK 900 RELATED ID: 1A5R RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION OF THE SMALL UBIQUITIN -RELATED MODIFIER REMARK 900 SUMO-1, NMR, 10 STRUCTURES REMARK 900 RELATED ID: 1TGZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1 REMARK 900 RELATED ID: 1WYW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO1-CONJUGATED THYMINE DNAGLYCOSYLASE REMARK 900 RELATED ID: 1Y8R RELATED DB: PDB REMARK 900 SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1- MG-ATP COMPLEX REMARK 900 RELATED ID: 1Z5S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN UBC9 , SUMO-1,RANGAP1 AND REMARK 900 NUP358/RANBP2 REMARK 900 RELATED ID: 2ASQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SUMO-1 IN COMPLEX WITH A SUMO-BINDINGMOTIF REMARK 900 (SBM) REMARK 900 RELATED ID: 2BF8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO MODIFIED UBIQUITIN CONJUGATING ENZYME E2- REMARK 900 25K REMARK 900 RELATED ID: 2IY0 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) SUMO1 RANGAP REMARK 900 RELATED ID: 2IYC RELATED DB: PDB REMARK 900 SENP1 NATIVE STRUCTURE REMARK 900 RELATED ID: 2IYD RELATED DB: PDB REMARK 900 SENP1 COVALENT COMPLEX WITH SUMO-2 DBREF 2IY1 A 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IY1 A 593 593 PDB 2IY1 2IY1 593 593 DBREF 2IY1 A 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 DBREF 2IY1 B 15 96 UNP P63165 SUMO1_HUMAN 20 101 DBREF 2IY1 B 97 97 PDB 2IY1 2IY1 97 97 DBREF 2IY1 C 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IY1 C 593 593 PDB 2IY1 2IY1 593 593 DBREF 2IY1 C 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 DBREF 2IY1 D 15 96 UNP P63165 SUMO1_HUMAN 20 101 DBREF 2IY1 D 97 97 PDB 2IY1 2IY1 97 97 SEQADV 2IY1 ALA A 603 UNP Q9P0U3 CYS 602 ENGINEERED MUTATION SEQADV 2IY1 ALA C 603 UNP Q9P0U3 CYS 602 ENGINEERED MUTATION SEQRES 1 A 226 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 A 226 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 A 226 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 A 226 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 A 226 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 A 226 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 A 226 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 A 226 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 A 226 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 A 226 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 A 226 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 A 226 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 A 226 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 A 226 SER LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SEQRES 15 A 226 SER ASP ALA GLY MET PHE ALA CYS LYS TYR ALA ASP CYS SEQRES 16 A 226 ILE THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS SEQRES 17 A 226 MET PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU SEQRES 18 A 226 HIS ARG LYS LEU LEU SEQRES 1 B 83 GLU TYR ILE LYS LEU LYS VAL ILE GLY GLN ASP SER SER SEQRES 2 B 83 GLU ILE HIS PHE LYS VAL LYS MET THR THR HIS LEU LYS SEQRES 3 B 83 LYS LEU LYS GLU SER TYR CYS GLN ARG GLN GLY VAL PRO SEQRES 4 B 83 MET ASN SER LEU ARG PHE LEU PHE GLU GLY GLN ARG ILE SEQRES 5 B 83 ALA ASP ASN HIS THR PRO LYS GLU LEU GLY MET GLU GLU SEQRES 6 B 83 GLU ASP VAL ILE GLU VAL TYR GLN GLU GLN THR GLY GLY SEQRES 7 B 83 HIS SER THR VAL CYS SEQRES 1 C 226 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 C 226 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 C 226 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 C 226 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 C 226 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 C 226 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 C 226 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 C 226 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 C 226 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 C 226 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 C 226 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 C 226 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 C 226 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 C 226 SER LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SEQRES 15 C 226 SER ASP ALA GLY MET PHE ALA CYS LYS TYR ALA ASP CYS SEQRES 16 C 226 ILE THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS SEQRES 17 C 226 MET PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU SEQRES 18 C 226 HIS ARG LYS LEU LEU SEQRES 1 D 83 GLU TYR ILE LYS LEU LYS VAL ILE GLY GLN ASP SER SER SEQRES 2 D 83 GLU ILE HIS PHE LYS VAL LYS MET THR THR HIS LEU LYS SEQRES 3 D 83 LYS LEU LYS GLU SER TYR CYS GLN ARG GLN GLY VAL PRO SEQRES 4 D 83 MET ASN SER LEU ARG PHE LEU PHE GLU GLY GLN ARG ILE SEQRES 5 D 83 ALA ASP ASN HIS THR PRO LYS GLU LEU GLY MET GLU GLU SEQRES 6 D 83 GLU ASP VAL ILE GLU VAL TYR GLN GLU GLN THR GLY GLY SEQRES 7 D 83 HIS SER THR VAL CYS FORMUL 5 HOH *113(H2 O) HELIX 1 1 THR A 424 PHE A 435 1 12 HELIX 2 2 ARG A 454 THR A 459 1 6 HELIX 3 3 ASN A 467 SER A 482 1 16 HELIX 4 4 PHE A 496 ALA A 504 1 9 HELIX 5 5 GLY A 505 VAL A 509 5 5 HELIX 6 6 VAL A 509 LYS A 514 5 6 HELIX 7 7 ASP A 517 VAL A 521 5 5 HELIX 8 8 ASN A 556 ARG A 576 1 21 HELIX 9 9 ASP A 602 LYS A 616 1 15 HELIX 10 10 THR A 623 GLN A 625 5 3 HELIX 11 11 HIS A 626 HIS A 640 1 15 HELIX 12 12 LEU B 39 GLY B 51 1 13 HELIX 13 13 PRO B 53 ASN B 55 5 3 HELIX 14 14 THR B 71 GLY B 76 1 6 HELIX 15 15 THR C 424 PHE C 435 1 12 HELIX 16 16 ARG C 454 GLN C 458 1 5 HELIX 17 17 THR C 459 ASN C 461 5 3 HELIX 18 18 ASN C 467 SER C 482 1 16 HELIX 19 19 PHE C 496 ALA C 504 1 9 HELIX 20 20 GLY C 505 VAL C 509 5 5 HELIX 21 21 VAL C 509 LYS C 514 5 6 HELIX 22 22 ASP C 517 VAL C 521 5 5 HELIX 23 23 ASN C 556 ARG C 576 1 21 HELIX 24 24 ASP C 602 LYS C 616 1 15 HELIX 25 25 THR C 623 GLN C 625 5 3 HELIX 26 26 HIS C 626 HIS C 640 1 15 HELIX 27 27 LEU D 39 GLY D 51 1 13 HELIX 28 28 PRO D 53 ASN D 55 5 3 HELIX 29 29 THR D 71 GLY D 76 1 6 SHEET 1 AA 2 VAL A 443 ALA A 447 0 SHEET 2 AA 2 LEU A 450 THR A 453 -1 O LEU A 450 N ALA A 447 SHEET 1 AB 5 VAL A 490 ALA A 492 0 SHEET 2 AB 5 ILE A 523 HIS A 529 1 O ILE A 523 N HIS A 491 SHEET 3 AB 5 TRP A 534 ASP A 540 -1 O CYS A 535 N ILE A 528 SHEET 4 AB 5 ASN A 545 TYR A 549 -1 O ASN A 545 N ASP A 540 SHEET 5 AB 5 GLN A 585 SER A 588 1 O GLN A 585 N ILE A 546 SHEET 1 BA 5 GLU B 28 VAL B 33 0 SHEET 2 BA 5 ILE B 17 ILE B 22 -1 O ILE B 17 N VAL B 33 SHEET 3 BA 5 ASP B 81 GLN B 87 1 O ASP B 81 N LYS B 20 SHEET 4 BA 5 LEU B 57 PHE B 61 -1 O ARG B 58 N TYR B 86 SHEET 5 BA 5 GLN B 64 ARG B 65 -1 O GLN B 64 N PHE B 61 SHEET 1 CA 2 VAL C 443 ALA C 447 0 SHEET 2 CA 2 LEU C 450 THR C 453 -1 O LEU C 450 N ALA C 447 SHEET 1 CB 5 VAL C 490 ALA C 492 0 SHEET 2 CB 5 ILE C 523 HIS C 529 1 O ILE C 523 N HIS C 491 SHEET 3 CB 5 TRP C 534 ASP C 540 -1 O CYS C 535 N ILE C 528 SHEET 4 CB 5 ASN C 545 TYR C 549 -1 O ASN C 545 N ASP C 540 SHEET 5 CB 5 GLN C 585 SER C 588 1 O GLN C 585 N ILE C 546 SHEET 1 DA 5 GLU D 28 VAL D 33 0 SHEET 2 DA 5 ILE D 17 GLY D 23 -1 O ILE D 17 N VAL D 33 SHEET 3 DA 5 VAL D 82 GLN D 87 1 O ILE D 83 N ILE D 22 SHEET 4 DA 5 LEU D 57 PHE D 61 -1 O ARG D 58 N TYR D 86 SHEET 5 DA 5 GLN D 64 ARG D 65 -1 O GLN D 64 N PHE D 61 CRYST1 141.232 141.232 98.964 90.00 90.00 90.00 P 43 21 2 16 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 0.007081 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010105 0.00000