HEADER LIGASE 06-DEC-04 2BF8 TITLE CRYSTAL STRUCTURE OF SUMO MODIFIED UBIQUITIN CONJUGATING ENZYME E2- TITLE 2 25K COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-25 KDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CONSERVED CORE DOMAIN, RESIDUES 1-154; COMPND 5 SYNONYM: E2-25K, UBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN, COMPND 6 E2(25K), HUNTINGTIN INTERACTING PROTEIN 2, HIP-2; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND COMPND 10 SUMO C-TERMINUS; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN-LIKE PROTEIN SMT3C; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: RESIDUES 21-97; COMPND 15 SYNONYM: SUMO, UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE COMPND 16 PROTEIN UBL1, UBIQUITIN-RELATED PROTEIN SUMO-1, GAP MODIFYING PROTEIN COMPND 17 1, GMP1, SENTRIN; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND COMPND 20 SUMO C-TERMINUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM30; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS LIGASE-COMPLEX, E2-25K, E2 UBIQUITIN CONJUGATING ENZYME, SUMO, SUMO- KEYWDS 2 TARGET STRUCTURE, LIGASE, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, KEYWDS 3 STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR A.PICHLER,P.KNIPSCHEER,E.OBERHOFER,W.J.VAN DIJK,R.KORNER,J.VELGAARD AUTHOR 2 OLSEN,S.JENTSCH,F.MELCHIOR,T.K.SIXMA REVDAT 5 13-DEC-23 2BF8 1 REMARK REVDAT 4 13-JUL-11 2BF8 1 VERSN REVDAT 3 24-FEB-09 2BF8 1 VERSN REVDAT 2 15-JUN-05 2BF8 1 JRNL REVDAT 1 16-FEB-05 2BF8 0 JRNL AUTH A.PICHLER,P.KNIPSCHEER,E.OBERHOFER,W.J.VAN DIJK,R.KORNER, JRNL AUTH 2 J.VELGAARD OLSEN,S.JENTSCH,F.MELCHIOR,T.K.SIXMA JRNL TITL SUMO IMODIFICATION OF THE UBIQUITIN CONJUGATING ENZYME JRNL TITL 2 E2-25K JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 264 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15723079 JRNL DOI 10.1038/NSMB903 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12545 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 651 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 871 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.4110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1853 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 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) : 53.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.04000 REMARK 3 B22 (A**2) : -2.04000 REMARK 3 B33 (A**2) : 4.07000 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): 0.315 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.029 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1905 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1729 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2577 ; 1.640 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4052 ; 0.927 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 7.276 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 91 ;35.697 ;25.055 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 347 ;17.644 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.630 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2095 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 360 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 403 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1782 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 900 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1064 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 91 ; 0.165 ; 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): 6 ; 0.075 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 27 ; 0.272 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.319 ; 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): 1512 ; 0.813 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 467 ; 0.173 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1884 ; 0.979 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 866 ; 1.755 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 693 ; 2.496 ; 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 1 A 155 REMARK 3 ORIGIN FOR THE GROUP (A): 40.1950 17.7830 69.7720 REMARK 3 T TENSOR REMARK 3 T11: -0.1357 T22: -0.2368 REMARK 3 T33: -0.2961 T12: -0.1081 REMARK 3 T13: 0.0391 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 3.5484 L22: 9.4825 REMARK 3 L33: 3.3554 L12: -1.0822 REMARK 3 L13: -1.9575 L23: 2.9418 REMARK 3 S TENSOR REMARK 3 S11: 0.0625 S12: -0.0756 S13: -0.0922 REMARK 3 S21: 0.4331 S22: -0.1307 S23: -0.7976 REMARK 3 S31: 0.3162 S32: -0.1059 S33: 0.0682 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): 17.9910 52.2470 74.2110 REMARK 3 T TENSOR REMARK 3 T11: 0.3663 T22: 0.3577 REMARK 3 T33: 0.1638 T12: 0.1206 REMARK 3 T13: 0.0810 T23: 0.3002 REMARK 3 L TENSOR REMARK 3 L11: 4.7404 L22: 9.4991 REMARK 3 L33: 8.4715 L12: -4.0568 REMARK 3 L13: -2.5666 L23: 0.2981 REMARK 3 S TENSOR REMARK 3 S11: 0.7684 S12: 1.0786 S13: 1.1827 REMARK 3 S21: -0.7803 S22: -0.4570 S23: -0.4250 REMARK 3 S31: -1.6759 S32: -0.7391 S33: -0.3114 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2BF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1290021807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 20 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111), SI(311) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : ADSC ADSC Q4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13257 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FZY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8.5 200 MM MAGNESIUM REMARK 280 CHLORIDE 17% PEG 4000 10 % GLYCEROL, PH 8.50 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 81.42100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.19550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.19550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 122.13150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.19550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.19550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.71050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.19550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.19550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 122.13150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.19550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.19550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.71050 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 81.42100 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 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 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 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 1.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ALA A 119 NH1 ARG B 54 7556 2.11 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 ASP A 30 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 48 CB - CG - OD2 ANGL. DEV. = 5.5 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 LYS A 97 -113.98 -124.09 REMARK 500 ALA A 119 88.36 -155.51 REMARK 500 ASN A 137 72.95 -151.02 REMARK 500 SER B 31 17.97 93.73 REMARK 500 THR B 41 55.61 -110.08 REMARK 500 ASN B 60 -8.44 84.58 REMARK 500 LEU B 80 -15.63 66.72 REMARK 500 REMARK 500 REMARK: NULL 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: 1TGZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1 REMARK 900 RELATED ID: 2BEP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBIQUITIN CONJUGATING ENZYME E2-25K REMARK 999 REMARK 999 SEQUENCE REMARK 999 COVALENT ISOPEPTIDE BOND BETWEEN E2-25K LYSINE 14 AND SUMO REMARK 999 C-TERMINUS DBREF 2BF8 A -3 1 PDB 2BF8 2BF8 -3 1 DBREF 2BF8 A 2 155 UNP P61085 UBC1_BOVIN 1 154 DBREF 2BF8 B 21 97 UNP P63165 SM33_HUMAN 21 97 SEQRES 1 A 159 GLY ALA MET ALA MET ALA ASN ILE ALA VAL GLN ARG ILE SEQRES 2 A 159 LYS ARG GLU PHE LYS GLU VAL LEU LYS SER GLU GLU THR SEQRES 3 A 159 SER LYS ASN GLN ILE LYS VAL ASP LEU VAL ASP GLU ASN SEQRES 4 A 159 PHE THR GLU LEU ARG GLY GLU ILE ALA GLY PRO PRO ASP SEQRES 5 A 159 THR PRO TYR GLU GLY GLY ARG TYR GLN LEU GLU ILE LYS SEQRES 6 A 159 ILE PRO GLU THR TYR PRO PHE ASN PRO PRO LYS VAL ARG SEQRES 7 A 159 PHE ILE THR LYS ILE TRP HIS PRO ASN ILE SER SER VAL SEQRES 8 A 159 THR GLY ALA ILE CYS LEU ASP ILE LEU LYS ASP GLN TRP SEQRES 9 A 159 ALA ALA ALA MET THR LEU ARG THR VAL LEU LEU SER LEU SEQRES 10 A 159 GLN ALA LEU LEU ALA ALA ALA GLU PRO ASP ASP PRO GLN SEQRES 11 A 159 ASP ALA VAL VAL ALA ASN GLN TYR LYS GLN ASN PRO GLU SEQRES 12 A 159 MET PHE LYS GLN THR ALA ARG LEU TRP ALA HIS VAL TYR SEQRES 13 A 159 ALA GLY ALA SEQRES 1 B 77 TYR ILE LYS LEU LYS VAL ILE GLY GLN ASP SER SER GLU SEQRES 2 B 77 ILE HIS PHE LYS VAL LYS MET THR THR HIS LEU LYS LYS SEQRES 3 B 77 LEU LYS GLU SER TYR CYS GLN ARG GLN GLY VAL PRO MET SEQRES 4 B 77 ASN SER LEU ARG PHE LEU PHE GLU GLY GLN ARG ILE ALA SEQRES 5 B 77 ASP ASN HIS THR PRO LYS GLU LEU GLY MET GLU GLU GLU SEQRES 6 B 77 ASP VAL ILE GLU VAL TYR GLN GLU GLN THR GLY GLY FORMUL 3 HOH *83(H2 O) HELIX 1 1 ALA A 2 LYS A 18 1 17 HELIX 2 2 SER A 19 LYS A 24 1 6 HELIX 3 3 LEU A 93 LYS A 97 5 5 HELIX 4 4 THR A 105 ALA A 119 1 15 HELIX 5 5 ASP A 127 ASN A 137 1 11 HELIX 6 6 ASN A 137 TYR A 152 1 16 HELIX 7 7 LEU B 44 GLN B 55 1 12 HELIX 8 8 LYS B 78 MET B 82 5 5 SHEET 1 AA 4 ILE A 27 LEU A 31 0 SHEET 2 AA 4 GLU A 38 ALA A 44 -1 O ARG A 40 N ASP A 30 SHEET 3 AA 4 ARG A 55 LYS A 61 -1 O TYR A 56 N ILE A 43 SHEET 4 AA 4 LYS A 72 PHE A 75 -1 O LYS A 72 N LYS A 61 SHEET 1 BA 5 GLU B 33 VAL B 38 0 SHEET 2 BA 5 ILE B 22 ILE B 27 -1 O ILE B 22 N VAL B 38 SHEET 3 BA 5 ASP B 86 GLN B 92 1 O ASP B 86 N LYS B 25 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 CISPEP 1 TYR A 66 PRO A 67 0 1.19 CRYST1 58.391 58.391 162.842 90.00 90.00 90.00 P 43 21 2 8 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 0.017126 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006141 0.00000