PDB Short entry for 2IYD HEADER HYDROLASE 14-JUL-06 2IYD TITLE SENP1 COVALENT COMPLEX WITH SUMO-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC 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 MOL_ID: 2; COMPND 9 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 2; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: CATALYTIC FRAGMENT, RESIDUES 15-95; COMPND 12 SYNONYM: SUMO2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, COMPND 13 SENTRIN-2, HSMT3, SUMO-2; COMPND 14 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 PROTEASE, HYDROLASE, THIOL PROTEASE, NUCLEAR PROTEIN, UBL KEYWDS 2 CONJUGATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,J.H.NAISMITH REVDAT 3 13-JUL-11 2IYD 1 VERSN REVDAT 2 24-FEB-09 2IYD 1 VERSN REVDAT 1 08-AUG-06 2IYD 0 JRNL AUTH C.DONG,J.H.NAISMITH JRNL TITL SENP1 NATIVE STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.SHEN,C.DONG,H.LIU,J.H.NAISMITH,R.T.HAY REMARK 1 TITL THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A REMARK 1 TITL 2 STRUCTURAL BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES REMARK 1 TITL 3 DURING PROCESSING REMARK 1 REF BIOCHEM.J. V. 397 279 2006 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 16553580 REMARK 1 DOI 10.1042/BJ20052030 REMARK 2 REMARK 2 RESOLUTION. 3.2 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13468 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) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.272 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 714 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : 0 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) : 107.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.13000 REMARK 3 B12 (A**2) : 0.04000 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): 0.581 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.407 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.378 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 54.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2577 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3462 ; 1.081 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 6.353 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;39.261 ;24.519 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;20.814 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 368 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1944 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1386 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1767 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 94 ; 0.147 ; 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): 23 ; 0.240 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.170 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 419 A 644 REMARK 3 ORIGIN FOR THE GROUP (A): 67.7985 -16.3022 18.3553 REMARK 3 T TENSOR REMARK 3 T11: -0.0604 T22: -0.3356 REMARK 3 T33: -0.5749 T12: 0.0643 REMARK 3 T13: 0.1063 T23: 0.0852 REMARK 3 L TENSOR REMARK 3 L11: 5.9434 L22: 9.7263 REMARK 3 L33: 2.9872 L12: -0.8523 REMARK 3 L13: -1.2751 L23: -0.4233 REMARK 3 S TENSOR REMARK 3 S11: -0.3692 S12: -0.5039 S13: -0.3427 REMARK 3 S21: 0.7041 S22: 0.2495 S23: 0.4621 REMARK 3 S31: 0.3100 S32: -0.0507 S33: 0.1197 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 14 B 92 REMARK 3 ORIGIN FOR THE GROUP (A): 54.1951 -23.1124 -1.5351 REMARK 3 T TENSOR REMARK 3 T11: 0.2177 T22: -0.1873 REMARK 3 T33: -0.2598 T12: -0.2746 REMARK 3 T13: -0.1054 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 5.6794 L22: 7.5373 REMARK 3 L33: 11.1390 L12: -2.4032 REMARK 3 L13: 5.7171 L23: 0.5961 REMARK 3 S TENSOR REMARK 3 S11: -0.3804 S12: 0.5824 S13: -0.6515 REMARK 3 S21: -1.1167 S22: 0.0152 S23: 1.3855 REMARK 3 S31: -1.0442 S32: -0.0727 S33: 0.3652 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 REMARK 3 RIDING POSITIONS. ONLY AN OVERALL B FACTOR REFINED THIS REMARK 3 REPLACES PREVIOUS ENTRY WHICH HAD SEQUENCE CONFLICTS. THERE IS REMARK 3 COVALENT LINK BETWEEN CYS A 603 (SENP1) AND GLY B 92 (SUMO) REMARK 3 THE DICTIONARY IS INCLUDED IN ENTRY REMARK 4 REMARK 4 2IYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-06. REMARK 100 THE PDBE ID CODE IS EBI-29390. 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) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13469 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 120.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):6.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 47.92400 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 23.96200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.96200 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 47.92400 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 VAL B 93 REMARK 465 TYR B 94 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 SG CYS A 603 CA GLY B 92 2.08 REMARK 500 SG CYS A 603 C GLY B 92 1.71 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 ASN A 439 96.87 60.86 REMARK 500 SER A 445 113.51 161.18 REMARK 500 ARG A 449 12.78 48.69 REMARK 500 HIS A 462 -103.32 49.09 REMARK 500 SER A 482 -167.17 -65.05 REMARK 500 LYS A 483 -13.11 51.40 REMARK 500 ASN A 494 149.82 -29.94 REMARK 500 PHE A 496 -9.61 -59.54 REMARK 500 PHE A 497 -71.15 -54.62 REMARK 500 LYS A 510 -74.41 -26.76 REMARK 500 VAL A 516 113.11 -172.54 REMARK 500 VAL A 518 -9.21 -59.84 REMARK 500 ASN A 599 -168.63 -113.87 REMARK 500 ASP A 617 -1.94 51.60 REMARK 500 THR A 623 -161.18 -119.57 REMARK 500 GLN A 625 -53.37 -25.67 REMARK 500 ARG A 641 67.40 63.34 REMARK 500 GLU B 48 -73.26 -58.32 REMARK 500 SER B 53 -78.21 -42.95 REMARK 500 MET B 54 -70.29 119.99 REMARK 500 ARG B 55 37.14 -79.00 REMARK 500 GLN B 56 9.72 -153.70 REMARK 500 ILE B 57 -169.86 -124.18 REMARK 500 GLN B 74 35.30 -82.77 REMARK 500 LEU B 75 -6.54 -141.07 REMARK 500 GLU B 80 7.54 52.06 REMARK 500 GLN B 89 120.90 73.63 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 REMARK 900 SUGGESTS A STRUCTURAL BASIS FOR DISCRIMINATION REMARK 900 BETWEEN SUMO PARALOGUES DURING PROCESSING REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX REMARK 900 RELATED ID: 1WM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN REMARK 900 RELATED ID: 1WM3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN REMARK 900 RELATED ID: 1WZ0 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUMAN SUMO-2 (SMT3B REMARK 900 ), A UBIQUITIN-LIKE PROTEIN REMARK 900 RELATED ID: 2IY0 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) SUMO1 RANGAP REMARK 900 RELATED ID: 2IY1 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) FULL LENGTH SUMO1 REMARK 900 RELATED ID: 2IYC RELATED DB: PDB REMARK 900 SENP1 NATIVE STRUCTURE REMARK 900 RELATED ID: 2D07 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO-3-MODIFIED THYMINE REMARK 900 -DNA GLYCOSYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS REMARK 999 A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED IN REMARK 999 PUBMED ID: 12477932. DBREF 2IYD A 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IYD A 593 593 PDB 2IYD 2IYD 593 593 DBREF 2IYD A 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 DBREF 2IYD B 14 94 UNP P61956 SUMO2_HUMAN 15 95 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 CYS 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 81 ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY GLN ASP GLY SEQRES 2 B 81 SER VAL VAL GLN PHE LYS ILE LYS ARG HIS THR PRO LEU SEQRES 3 B 81 SER LYS LEU MET LYS ALA TYR CYS GLU ARG GLN GLY LEU SEQRES 4 B 81 SER MET ARG GLN ILE ARG PHE ARG PHE ASP GLY GLN PRO SEQRES 5 B 81 ILE ASN GLU THR ASP THR PRO ALA GLN LEU GLU MET GLU SEQRES 6 B 81 ASP GLU ASP THR ILE ASP VAL PHE GLN GLN GLN THR GLY SEQRES 7 B 81 GLY VAL TYR HELIX 1 1 THR A 424 ARG A 436 1 13 HELIX 2 2 ARG A 454 THR A 459 1 6 HELIX 3 3 ASN A 467 ARG A 481 1 15 HELIX 4 4 PHE A 496 GLY A 505 1 10 HELIX 5 5 GLY A 505 LYS A 510 1 6 HELIX 6 6 ARG A 511 LYS A 514 5 4 HELIX 7 7 ASN A 556 LYS A 575 1 20 HELIX 8 8 ASP A 602 LYS A 616 1 15 HELIX 9 9 HIS A 626 ARG A 641 1 16 HELIX 10 10 LEU B 39 ARG B 49 1 11 HELIX 11 11 PRO B 72 GLU B 76 5 5 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 LEU A 530 1 O ILE A 523 N HIS A 491 SHEET 3 AB 5 HIS A 533 ASP A 540 -1 O HIS A 533 N LEU A 530 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 SER B 27 LYS B 34 0 SHEET 2 BA 5 HIS B 16 GLY B 23 -1 O ILE B 17 N ILE 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 ILE B 57 PHE B 61 -1 O ARG B 58 N PHE B 86 SHEET 5 BA 5 GLN B 64 PRO B 65 -1 O GLN B 64 N PHE B 61 CRYST1 143.376 143.376 71.886 90.00 90.00 120.00 P 32 2 1 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 0.006975 0.004027 0.000000 0.00000 SCALE2 0.000000 0.008054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013911 0.00000