PDB Short entry for 2VRR HEADER CELL CYCLE/LIGASE 13-APR-08 2VRR TITLE STRUCTURE OF SUMO MODIFIED UBC9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUMO-CONJUGATING ENZYME UBC9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBC9, SUMO-PROTEIN LIGASE, UBIQUITIN-CONJUGATING ENZYME E2 COMPND 5 I, UBIQUITIN-PROTEIN LIGASE I, UBIQUITIN CARRIER PROTEIN I, UBIQUITIN COMPND 6 CARRIER PROTEIN 9, MUBC9; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 20-97; COMPND 13 SYNONYM: SUMO1, SUMO-1, SENTRIN, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3 COMPND 14 HOMOLOG 3, UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE COMPND 15 PROTEIN UBL1, GAP-MODIFYING PROTEIN 1, GMP1; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET23A; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS E2, UBC9, SUMO, LIGASE, NUCLEUS, MITOSIS, MEMBRANE, PHOSPHOPROTEIN, KEYWDS 2 ISOPEPTIDE BOND, CHROMOSOME PARTITION, POSTTRANSLATIONAL KEYWDS 3 MODIFICATION, UBL CONJUGATION PATHWAY, UBIQUITIN LIKE MOLECULE, KEYWDS 4 DEVELOPMENTAL PROTEIN, HOST-VIRUS INTERACTION, CYTOPLASM, CELL KEYWDS 5 CYCLE, MODIFICATION, CELL DIVISION, CELL CYCLE/LIGASE, CELL CYCLE- KEYWDS 6 LIGASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.KNIPSCHEER,A.FLOTHO,H.KLUG,J.V.OLSEN,W.J.VAN DIJK,A.FISH, AUTHOR 2 E.S.JOHNSON,M.MANN,T.K.SIXMA,A.PICHLER REVDAT 6 13-DEC-23 2VRR 1 REMARK REVDAT 5 31-JUL-19 2VRR 1 REMARK LINK REVDAT 4 28-MAR-18 2VRR 1 SOURCE JRNL REVDAT 3 28-JUN-17 2VRR 1 REMARK REVDAT 2 24-FEB-09 2VRR 1 VERSN REVDAT 1 19-AUG-08 2VRR 0 JRNL AUTH P.KNIPSCHEER,A.FLOTHO,H.KLUG,J.V.OLSEN,W.J.VAN DIJK,A.FISH, JRNL AUTH 2 E.S.JOHNSON,M.MANN,T.K.SIXMA,A.PICHLER JRNL TITL UBC9 SUMOYLATION REGULATES SUMO TARGET DISCRIMINATION. JRNL REF MOL. CELL V. 31 371 2008 JRNL REFN ISSN 1097-4164 JRNL PMID 18691969 JRNL DOI 10.1016/J.MOLCEL.2008.05.022 REMARK 2 REMARK 2 RESOLUTION. 2.22 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 11169 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 761 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1904 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.355 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.002 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2012 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1437 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2717 ; 1.633 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3520 ; 0.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 245 ; 6.439 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;32.036 ;24.842 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;15.373 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.404 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 280 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2236 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 387 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 393 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1460 ; 0.198 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 925 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1045 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 156 ; 0.179 ; 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): 24 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.274 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.175 ; 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): 1220 ; 0.636 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1973 ; 1.092 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 818 ; 1.986 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 743 ; 3.118 ; 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 : 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 2 A 158 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3920 6.7180 10.1160 REMARK 3 T TENSOR REMARK 3 T11: -0.1433 T22: -0.0695 REMARK 3 T33: -0.1907 T12: -0.0117 REMARK 3 T13: -0.0032 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 1.6245 L22: 2.1545 REMARK 3 L33: 1.3649 L12: -0.4178 REMARK 3 L13: -0.1072 L23: -0.4135 REMARK 3 S TENSOR REMARK 3 S11: -0.0237 S12: -0.0749 S13: -0.1619 REMARK 3 S21: 0.0542 S22: -0.0274 S23: -0.0002 REMARK 3 S31: 0.1660 S32: 0.0562 S33: 0.0511 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 20 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6290 39.3670 25.3410 REMARK 3 T TENSOR REMARK 3 T11: -0.0685 T22: -0.0225 REMARK 3 T33: -0.1560 T12: -0.0103 REMARK 3 T13: 0.0236 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 5.2598 L22: 7.2342 REMARK 3 L33: 3.5148 L12: -1.2100 REMARK 3 L13: 0.7842 L23: 2.2124 REMARK 3 S TENSOR REMARK 3 S11: -0.0624 S12: 0.1312 S13: 0.2994 REMARK 3 S21: -0.1458 S22: -0.0046 S23: -0.0757 REMARK 3 S31: -0.2776 S32: -0.0582 S33: 0.0669 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 RIDING REMARK 3 POSITIONS RESIDUES B94-B96 ARE DISORDERED AND HAVE BEEN GIVEN AN REMARK 3 OCCUPANCY OF 0. THERE IS A COVALENT ISOPEPTIDE LINKAGE BETWEEN REMARK 3 LYSINE A14 AND GLYCINE B97 REMARK 4 REMARK 4 2VRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290035810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : HELIOS MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRIES 1U9B, 2BF8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG3350, 200 MM SODIUM REMARK 280 FORMATE, 100 MM BIS-TRIS PROPANE PH6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 13.76000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.28950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.28950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.30500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.4 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 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 1 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLN B 94 REMARK 475 THR B 95 REMARK 475 GLY B 96 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 14 C GLY B 97 1.34 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 B 20 CG GLU B 20 CD 0.125 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 ARG B 63 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ASP A 19 122.51 -174.57 REMARK 500 ALA A 26 102.26 -160.93 REMARK 500 HIS A 83 138.43 179.42 REMARK 500 LYS A 101 -104.40 -106.72 REMARK 500 ILE A 125 -4.85 -59.10 REMARK 500 ASN B 60 1.25 -69.64 REMARK 500 GLU B 85 18.84 55.26 REMARK 500 GLN B 94 -62.51 109.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B1098 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B1099 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1159 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1161 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2ASQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SUMO-1 IN COMPLEX WITH A SUMO-BINDINGMOTIF REMARK 900 (SBM) REMARK 900 RELATED ID: 2UYZ RELATED DB: PDB REMARK 900 NON-COVALENT COMPLEX BETWEEN UBC9 AND SUMO1 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: 1U9A RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 REMARK 900 RELATED ID: 2IY1 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) FULL LENGTH SUMO1 REMARK 900 RELATED ID: 1TGZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1 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: 2IY0 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) SUMO1 RANGAP REMARK 900 RELATED ID: 1WYW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO1-CONJUGATED THYMINE DNAGLYCOSYLASE REMARK 900 RELATED ID: 1U9B RELATED DB: PDB REMARK 900 MURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 REMARK 900 RELATED ID: 2IO2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1-SUMO-1 REMARK 900 RELATED ID: 1Y8R RELATED DB: PDB REMARK 900 SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1- MG-ATP COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE 20-97 OF SUMO1 PRECEDED BY A START METHIONINE DBREF 2VRR A 1 158 UNP P63280 UBC9_MOUSE 1 158 DBREF 2VRR B 19 19 PDB 2VRR 2VRR 19 19 DBREF 2VRR B 20 97 UNP P63165 SUMO1_HUMAN 20 97 SEQRES 1 A 158 MET SER GLY ILE ALA LEU SER ARG LEU ALA GLN GLU ARG SEQRES 2 A 158 LYS ALA TRP ARG LYS ASP HIS PRO PHE GLY PHE VAL ALA SEQRES 3 A 158 VAL PRO THR LYS ASN PRO ASP GLY THR MET ASN LEU MET SEQRES 4 A 158 ASN TRP GLU CYS ALA ILE PRO GLY LYS LYS GLY THR PRO SEQRES 5 A 158 TRP GLU GLY GLY LEU PHE LYS LEU ARG MET LEU PHE LYS SEQRES 6 A 158 ASP ASP TYR PRO SER SER PRO PRO LYS CYS LYS PHE GLU SEQRES 7 A 158 PRO PRO LEU PHE HIS PRO ASN VAL TYR PRO SER GLY THR SEQRES 8 A 158 VAL CYS LEU SER ILE LEU GLU GLU ASP LYS ASP TRP ARG SEQRES 9 A 158 PRO ALA ILE THR ILE LYS GLN ILE LEU LEU GLY ILE GLN SEQRES 10 A 158 GLU LEU LEU ASN GLU PRO ASN ILE GLN ASP PRO ALA GLN SEQRES 11 A 158 ALA GLU ALA TYR THR ILE TYR CYS GLN ASN ARG VAL GLU SEQRES 12 A 158 TYR GLU LYS ARG VAL ARG ALA GLN ALA LYS LYS PHE ALA SEQRES 13 A 158 PRO SER SEQRES 1 B 79 MET GLU TYR ILE LYS LEU LYS VAL ILE GLY GLN ASP SER SEQRES 2 B 79 SER GLU ILE HIS PHE LYS VAL LYS MET THR THR HIS LEU SEQRES 3 B 79 LYS LYS LEU LYS GLU SER TYR CYS GLN ARG GLN GLY VAL SEQRES 4 B 79 PRO MET ASN SER LEU ARG PHE LEU PHE GLU GLY GLN ARG SEQRES 5 B 79 ILE ALA ASP ASN HIS THR PRO LYS GLU LEU GLY MET GLU SEQRES 6 B 79 GLU GLU ASP VAL ILE GLU VAL TYR GLN GLU GLN THR GLY SEQRES 7 B 79 GLY HET FMT A1159 3 HET FMT A1160 3 HET NA A1161 1 HET FMT B1098 3 HET FMT B1099 3 HETNAM FMT FORMIC ACID HETNAM NA SODIUM ION FORMUL 3 FMT 4(C H2 O2) FORMUL 5 NA NA 1+ FORMUL 8 HOH *192(H2 O) HELIX 1 1 SER A 2 ASP A 19 1 18 HELIX 2 2 LEU A 94 GLU A 98 5 5 HELIX 3 3 THR A 108 GLU A 122 1 15 HELIX 4 4 GLN A 130 ASN A 140 1 11 HELIX 5 5 ASN A 140 PHE A 155 1 16 HELIX 6 6 LEU B 44 GLY B 56 1 13 HELIX 7 7 PRO B 58 ASN B 60 5 3 SHEET 1 AA 4 VAL A 25 LYS A 30 0 SHEET 2 AA 4 MET A 36 PRO A 46 -1 O ASN A 37 N THR A 29 SHEET 3 AA 4 LEU A 57 LEU A 63 -1 O PHE A 58 N ILE A 45 SHEET 4 AA 4 LYS A 74 PHE A 77 -1 O LYS A 74 N LEU A 63 SHEET 1 BA 5 GLU B 33 LYS B 39 0 SHEET 2 BA 5 TYR B 21 ILE B 27 -1 O ILE B 22 N VAL B 38 SHEET 3 BA 5 VAL B 87 GLN B 92 1 O ILE B 88 N ILE B 27 SHEET 4 BA 5 LEU B 62 PHE B 66 -1 O ARG B 63 N TYR B 91 SHEET 5 BA 5 GLN B 69 ARG B 70 -1 O GLN B 69 N PHE B 66 LINK NA NA A1161 O HOH A2097 1555 1555 3.19 CISPEP 1 TYR A 68 PRO A 69 0 1.59 CISPEP 2 GLU A 78 PRO A 79 0 1.25 CISPEP 3 MET B 19 GLU B 20 0 2.25 CISPEP 4 MET B 19 GLU B 20 0 8.61 CISPEP 5 GLN B 94 THR B 95 0 3.85 SITE 1 AC1 3 ARG B 70 GLU B 93 FMT B1099 SITE 1 AC2 2 GLU B 33 FMT B1098 SITE 1 AC3 2 ALA A 15 HOH A2012 SITE 1 AC4 5 LEU A 57 PHE A 58 LYS A 59 PHE A 155 SITE 2 AC4 5 HOH A2136 SITE 1 AC5 2 GLU A 99 ALA A 106 CRYST1 27.520 66.610 122.579 90.00 90.00 90.00 P 21 21 21 4 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 0.036337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008158 0.00000