PDB Short entry for 2IO1 HEADER PROTEIN BINDING, HYDROLASE 09-OCT-06 2IO1 TITLE CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 2; COMPND 3 CHAIN: A, C, E; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: SENTRIN/SUMO-SPECIFIC PROTEASE SENP2, SMT3-SPECIFIC COMPND 6 ISOPEPTIDASE 2, SMT3IP2, AXAM2; COMPND 7 EC: 3.4.22.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 3 PRECURSOR; COMPND 12 CHAIN: B, D, F; COMPND 13 SYNONYM: SUMO-3, UBIQUITIN-LIKE PROTEIN SMT3A, SMT3 HOMOLOG 1; 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 GENE: SENP2, KIAA1331; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: SUMO3, SMT3A, SMT3H1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS SUMO, UBIQUITIN, SENP, ULP, COMPLEX, PROTEIN BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.REVERTER,C.D.LIMA REVDAT 6 30-AUG-23 2IO1 1 REMARK REVDAT 5 20-OCT-21 2IO1 1 SEQADV REVDAT 4 18-OCT-17 2IO1 1 REMARK REVDAT 3 24-FEB-09 2IO1 1 VERSN REVDAT 2 02-JAN-07 2IO1 1 JRNL REVDAT 1 14-NOV-06 2IO1 0 JRNL AUTH D.REVERTER,C.D.LIMA JRNL TITL STRUCTURAL BASIS FOR SENP2 PROTEASE INTERACTIONS WITH SUMO JRNL TITL 2 PRECURSORS AND CONJUGATED SUBSTRATES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 1060 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 17099700 JRNL DOI 10.1038/NSMB1168 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2619913.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 38679 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 SET) : 0.204 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4384 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 217 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7538 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 278 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.68000 REMARK 3 B22 (A**2) : 2.80000 REMARK 3 B33 (A**2) : -9.48000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 29.79 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40430 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 ENTRY 1TGZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 4000, 0.1M SODIUM ACETATE, 0.2M REMARK 280 MAGNESIUM CHLORIDE, 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.06000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 70.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.68000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 70.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.68000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.06000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 70.99000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.68000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.06000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 70.99000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.68000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 3 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 358 REMARK 465 SER A 359 REMARK 465 HIS A 360 REMARK 465 MET A 361 REMARK 465 ALA A 362 REMARK 465 SER A 363 REMARK 465 ASP A 364 REMARK 465 LEU A 365 REMARK 465 LEU A 366 REMARK 465 GLY B 10 REMARK 465 SER B 11 REMARK 465 HIS B 12 REMARK 465 MET B 13 REMARK 465 ASN B 14 REMARK 465 SER B 96 REMARK 465 SER B 97 REMARK 465 LEU B 98 REMARK 465 ALA B 99 REMARK 465 GLY B 100 REMARK 465 HIS B 101 REMARK 465 SER B 102 REMARK 465 PHE B 103 REMARK 465 GLY C 358 REMARK 465 SER C 359 REMARK 465 HIS C 360 REMARK 465 MET C 361 REMARK 465 ALA C 362 REMARK 465 SER C 363 REMARK 465 ASP C 364 REMARK 465 LEU C 365 REMARK 465 GLY D 10 REMARK 465 SER D 11 REMARK 465 HIS D 12 REMARK 465 MET D 13 REMARK 465 ASN D 14 REMARK 465 SER D 97 REMARK 465 LEU D 98 REMARK 465 ALA D 99 REMARK 465 GLY D 100 REMARK 465 HIS D 101 REMARK 465 SER D 102 REMARK 465 PHE D 103 REMARK 465 GLY E 358 REMARK 465 SER E 359 REMARK 465 HIS E 360 REMARK 465 MET E 361 REMARK 465 ALA E 362 REMARK 465 SER E 363 REMARK 465 ASP E 364 REMARK 465 LEU E 365 REMARK 465 LEU E 366 REMARK 465 GLY F 10 REMARK 465 SER F 11 REMARK 465 HIS F 12 REMARK 465 MET F 13 REMARK 465 ASN F 14 REMARK 465 SER F 96 REMARK 465 SER F 97 REMARK 465 LEU F 98 REMARK 465 ALA F 99 REMARK 465 GLY F 100 REMARK 465 HIS F 101 REMARK 465 SER F 102 REMARK 465 PHE F 103 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 GLN F 50 O HOH F 113 2.18 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 NH2 ARG A 475 O GLU D 48 4555 2.17 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 THR A 369 158.46 -45.30 REMARK 500 TRP A 457 2.68 -64.73 REMARK 500 LYS A 476 -47.24 -20.36 REMARK 500 VAL A 477 24.65 -144.37 REMARK 500 ARG A 520 30.33 -140.86 REMARK 500 ASN A 521 75.49 25.41 REMARK 500 SER A 522 131.50 -176.29 REMARK 500 PRO A 536 -16.16 -47.11 REMARK 500 SER A 546 1.55 -159.74 REMARK 500 ILE A 565 94.63 -63.46 REMARK 500 LEU B 39 -2.10 -56.77 REMARK 500 ALA C 392 156.94 179.17 REMARK 500 LYS C 476 104.26 2.43 REMARK 500 HIS C 478 118.36 -174.98 REMARK 500 LYS C 489 53.73 39.90 REMARK 500 ILE C 565 102.79 -59.47 REMARK 500 ALA E 392 149.07 -178.17 REMARK 500 TYR E 408 -8.46 73.06 REMARK 500 GLN E 499 165.60 -45.92 REMARK 500 LEU E 526 -12.51 -48.80 REMARK 500 MET E 534 125.41 -33.73 REMARK 500 ALA F 45 -71.80 -53.44 REMARK 500 ARG F 49 12.75 -55.31 REMARK 500 GLN F 50 -1.54 -147.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1 REMARK 900 RELATED ID: 2IO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-2 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: 2IO3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1-SUMO-2 DBREF 2IO1 A 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO1 C 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO1 E 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO1 B 14 103 UNP P55854 SUMO3_HUMAN 14 103 DBREF 2IO1 D 14 103 UNP P55854 SUMO3_HUMAN 14 103 DBREF 2IO1 F 14 103 UNP P55854 SUMO3_HUMAN 14 103 SEQADV 2IO1 GLY A 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER A 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 HIS A 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 MET A 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 ALA A 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER A 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER A 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO1 GLY C 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER C 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 HIS C 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 MET C 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 ALA C 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER C 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER C 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO1 GLY E 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER E 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 HIS E 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 MET E 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 ALA E 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER E 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO1 SER E 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO1 GLY B 10 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 SER B 11 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 HIS B 12 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 MET B 13 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 GLY D 10 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 SER D 11 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 HIS D 12 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 MET D 13 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 GLY F 10 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 SER F 11 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 HIS F 12 UNP P55854 CLONING ARTIFACT SEQADV 2IO1 MET F 13 UNP P55854 CLONING ARTIFACT SEQRES 1 A 232 GLY SER HIS MET ALA SER ASP LEU LEU GLU LEU THR GLU SEQRES 2 A 232 ASP MET GLU LYS GLU ILE SER ASN ALA LEU GLY HIS GLY SEQRES 3 A 232 PRO GLN ASP GLU ILE LEU SER SER ALA PHE LYS LEU ARG SEQRES 4 A 232 ILE THR ARG GLY ASP ILE GLN THR LEU LYS ASN TYR HIS SEQRES 5 A 232 TRP LEU ASN ASP GLU VAL ILE ASN PHE TYR MET ASN LEU SEQRES 6 A 232 LEU VAL GLU ARG ASN LYS LYS GLN GLY TYR PRO ALA LEU SEQRES 7 A 232 HIS VAL PHE SER THR PHE PHE TYR PRO LYS LEU LYS SER SEQRES 8 A 232 GLY GLY TYR GLN ALA VAL LYS ARG TRP THR LYS GLY VAL SEQRES 9 A 232 ASN LEU PHE GLU GLN GLU ILE ILE LEU VAL PRO ILE HIS SEQRES 10 A 232 ARG LYS VAL HIS TRP SER LEU VAL VAL ILE ASP LEU ARG SEQRES 11 A 232 LYS LYS CYS LEU LYS TYR LEU ASP SER MET GLY GLN LYS SEQRES 12 A 232 GLY HIS ARG ILE CYS GLU ILE LEU LEU GLN TYR LEU GLN SEQRES 13 A 232 ASP GLU SER LYS THR LYS ARG ASN SER ASP LEU ASN LEU SEQRES 14 A 232 LEU GLU TRP THR HIS HIS SER MET LYS PRO HIS GLU ILE SEQRES 15 A 232 PRO GLN GLN LEU ASN GLY SER ASP SER GLY MET PHE THR SEQRES 16 A 232 CYS LYS TYR ALA ASP TYR ILE SER ARG ASP LYS PRO ILE SEQRES 17 A 232 THR PHE THR GLN HIS GLN MET PRO LEU PHE ARG LYS LYS SEQRES 18 A 232 MET VAL TRP GLU ILE LEU HIS GLN GLN LEU LEU SEQRES 1 B 94 GLY SER HIS MET ASN ASP HIS ILE ASN LEU LYS VAL ALA SEQRES 2 B 94 GLY GLN ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG SEQRES 3 B 94 HIS THR PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU SEQRES 4 B 94 ARG GLN GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE SEQRES 5 B 94 ASP GLY GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN SEQRES 6 B 94 LEU GLU MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN SEQRES 7 B 94 GLN GLN THR GLY GLY VAL PRO GLU SER SER LEU ALA GLY SEQRES 8 B 94 HIS SER PHE SEQRES 1 C 232 GLY SER HIS MET ALA SER ASP LEU LEU GLU LEU THR GLU SEQRES 2 C 232 ASP MET GLU LYS GLU ILE SER ASN ALA LEU GLY HIS GLY SEQRES 3 C 232 PRO GLN ASP GLU ILE LEU SER SER ALA PHE LYS LEU ARG SEQRES 4 C 232 ILE THR ARG GLY ASP ILE GLN THR LEU LYS ASN TYR HIS SEQRES 5 C 232 TRP LEU ASN ASP GLU VAL ILE ASN PHE TYR MET ASN LEU SEQRES 6 C 232 LEU VAL GLU ARG ASN LYS LYS GLN GLY TYR PRO ALA LEU SEQRES 7 C 232 HIS VAL PHE SER THR PHE PHE TYR PRO LYS LEU LYS SER SEQRES 8 C 232 GLY GLY TYR GLN ALA VAL LYS ARG TRP THR LYS GLY VAL SEQRES 9 C 232 ASN LEU PHE GLU GLN GLU ILE ILE LEU VAL PRO ILE HIS SEQRES 10 C 232 ARG LYS VAL HIS TRP SER LEU VAL VAL ILE ASP LEU ARG SEQRES 11 C 232 LYS LYS CYS LEU LYS TYR LEU ASP SER MET GLY GLN LYS SEQRES 12 C 232 GLY HIS ARG ILE CYS GLU ILE LEU LEU GLN TYR LEU GLN SEQRES 13 C 232 ASP GLU SER LYS THR LYS ARG ASN SER ASP LEU ASN LEU SEQRES 14 C 232 LEU GLU TRP THR HIS HIS SER MET LYS PRO HIS GLU ILE SEQRES 15 C 232 PRO GLN GLN LEU ASN GLY SER ASP SER GLY MET PHE THR SEQRES 16 C 232 CYS LYS TYR ALA ASP TYR ILE SER ARG ASP LYS PRO ILE SEQRES 17 C 232 THR PHE THR GLN HIS GLN MET PRO LEU PHE ARG LYS LYS SEQRES 18 C 232 MET VAL TRP GLU ILE LEU HIS GLN GLN LEU LEU SEQRES 1 D 94 GLY SER HIS MET ASN ASP HIS ILE ASN LEU LYS VAL ALA SEQRES 2 D 94 GLY GLN ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG SEQRES 3 D 94 HIS THR PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU SEQRES 4 D 94 ARG GLN GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE SEQRES 5 D 94 ASP GLY GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN SEQRES 6 D 94 LEU GLU MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN SEQRES 7 D 94 GLN GLN THR GLY GLY VAL PRO GLU SER SER LEU ALA GLY SEQRES 8 D 94 HIS SER PHE SEQRES 1 E 232 GLY SER HIS MET ALA SER ASP LEU LEU GLU LEU THR GLU SEQRES 2 E 232 ASP MET GLU LYS GLU ILE SER ASN ALA LEU GLY HIS GLY SEQRES 3 E 232 PRO GLN ASP GLU ILE LEU SER SER ALA PHE LYS LEU ARG SEQRES 4 E 232 ILE THR ARG GLY ASP ILE GLN THR LEU LYS ASN TYR HIS SEQRES 5 E 232 TRP LEU ASN ASP GLU VAL ILE ASN PHE TYR MET ASN LEU SEQRES 6 E 232 LEU VAL GLU ARG ASN LYS LYS GLN GLY TYR PRO ALA LEU SEQRES 7 E 232 HIS VAL PHE SER THR PHE PHE TYR PRO LYS LEU LYS SER SEQRES 8 E 232 GLY GLY TYR GLN ALA VAL LYS ARG TRP THR LYS GLY VAL SEQRES 9 E 232 ASN LEU PHE GLU GLN GLU ILE ILE LEU VAL PRO ILE HIS SEQRES 10 E 232 ARG LYS VAL HIS TRP SER LEU VAL VAL ILE ASP LEU ARG SEQRES 11 E 232 LYS LYS CYS LEU LYS TYR LEU ASP SER MET GLY GLN LYS SEQRES 12 E 232 GLY HIS ARG ILE CYS GLU ILE LEU LEU GLN TYR LEU GLN SEQRES 13 E 232 ASP GLU SER LYS THR LYS ARG ASN SER ASP LEU ASN LEU SEQRES 14 E 232 LEU GLU TRP THR HIS HIS SER MET LYS PRO HIS GLU ILE SEQRES 15 E 232 PRO GLN GLN LEU ASN GLY SER ASP SER GLY MET PHE THR SEQRES 16 E 232 CYS LYS TYR ALA ASP TYR ILE SER ARG ASP LYS PRO ILE SEQRES 17 E 232 THR PHE THR GLN HIS GLN MET PRO LEU PHE ARG LYS LYS SEQRES 18 E 232 MET VAL TRP GLU ILE LEU HIS GLN GLN LEU LEU SEQRES 1 F 94 GLY SER HIS MET ASN ASP HIS ILE ASN LEU LYS VAL ALA SEQRES 2 F 94 GLY GLN ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG SEQRES 3 F 94 HIS THR PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU SEQRES 4 F 94 ARG GLN GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE SEQRES 5 F 94 ASP GLY GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN SEQRES 6 F 94 LEU GLU MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN SEQRES 7 F 94 GLN GLN THR GLY GLY VAL PRO GLU SER SER LEU ALA GLY SEQRES 8 F 94 HIS SER PHE FORMUL 7 HOH *278(H2 O) HELIX 1 1 THR A 369 GLY A 381 1 13 HELIX 2 2 ARG A 399 GLN A 403 1 5 HELIX 3 3 THR A 404 LYS A 406 5 3 HELIX 4 4 ASP A 413 GLY A 431 1 19 HELIX 5 5 PHE A 441 LYS A 455 1 15 HELIX 6 6 ARG A 456 LYS A 459 5 4 HELIX 7 7 ASN A 462 GLN A 466 5 5 HELIX 8 8 GLY A 501 ASN A 521 1 21 HELIX 9 9 ASP A 547 ARG A 561 1 15 HELIX 10 10 GLN A 571 GLN A 586 1 16 HELIX 11 11 LEU B 39 GLY B 51 1 13 HELIX 12 12 SER B 53 ARG B 55 5 3 HELIX 13 13 THR C 369 GLY C 381 1 13 HELIX 14 14 ARG C 399 GLN C 403 1 5 HELIX 15 15 THR C 404 LYS C 406 5 3 HELIX 16 16 ASN C 412 GLY C 431 1 20 HELIX 17 17 PHE C 441 GLY C 450 1 10 HELIX 18 18 GLY C 450 LYS C 455 1 6 HELIX 19 19 ARG C 456 LYS C 459 5 4 HELIX 20 20 ASN C 462 GLN C 466 5 5 HELIX 21 21 GLY C 501 ASN C 521 1 21 HELIX 22 22 ASN C 525 TRP C 529 5 5 HELIX 23 23 ASP C 547 ARG C 561 1 15 HELIX 24 24 THR C 568 HIS C 570 5 3 HELIX 25 25 GLN C 571 GLN C 586 1 16 HELIX 26 26 LEU D 39 GLY D 51 1 13 HELIX 27 27 SER D 53 ARG D 55 5 3 HELIX 28 28 THR E 369 GLY E 381 1 13 HELIX 29 29 ARG E 399 GLN E 403 1 5 HELIX 30 30 THR E 404 LYS E 406 5 3 HELIX 31 31 ASP E 413 GLY E 431 1 19 HELIX 32 32 PHE E 441 GLY E 450 1 10 HELIX 33 33 GLY E 450 LYS E 455 1 6 HELIX 34 34 ARG E 456 LYS E 459 5 4 HELIX 35 35 ASN E 462 GLN E 466 5 5 HELIX 36 36 GLY E 501 ARG E 520 1 20 HELIX 37 37 ASN E 525 TRP E 529 5 5 HELIX 38 38 ASP E 547 SER E 560 1 14 HELIX 39 39 THR E 568 HIS E 570 5 3 HELIX 40 40 GLN E 571 GLN E 586 1 16 HELIX 41 41 LEU F 39 ARG F 49 1 11 SHEET 1 A 2 ILE A 388 ALA A 392 0 SHEET 2 A 2 LEU A 395 THR A 398 -1 O ILE A 397 N SER A 390 SHEET 1 B 2 LEU A 411 ASN A 412 0 SHEET 2 B 2 THR B 90 GLY B 91 -1 O GLY B 91 N LEU A 411 SHEET 1 C 5 LEU A 435 VAL A 437 0 SHEET 2 C 5 ILE A 468 ARG A 475 1 O LEU A 470 N HIS A 436 SHEET 3 C 5 HIS A 478 ASP A 485 -1 O SER A 480 N ILE A 473 SHEET 4 C 5 CYS A 490 LEU A 494 -1 O LEU A 494 N LEU A 481 SHEET 5 C 5 THR A 530 SER A 533 1 O THR A 530 N LEU A 491 SHEET 1 D 5 VAL B 28 LYS B 34 0 SHEET 2 D 5 HIS B 16 ALA B 22 -1 N ILE B 17 O ILE B 33 SHEET 3 D 5 THR B 82 GLN B 87 1 O ILE B 83 N LYS B 20 SHEET 4 D 5 ILE B 57 PHE B 61 -1 N ARG B 60 O ASP B 84 SHEET 5 D 5 GLN B 64 PRO B 65 -1 O GLN B 64 N PHE B 61 SHEET 1 E 2 ILE C 388 ALA C 392 0 SHEET 2 E 2 LEU C 395 THR C 398 -1 O ILE C 397 N SER C 390 SHEET 1 F 5 LEU C 435 VAL C 437 0 SHEET 2 F 5 ILE C 468 HIS C 474 1 O ILE C 468 N HIS C 436 SHEET 3 F 5 TRP C 479 ASP C 485 -1 O ILE C 484 N ILE C 469 SHEET 4 F 5 CYS C 490 LEU C 494 -1 O CYS C 490 N ASP C 485 SHEET 5 F 5 THR C 530 SER C 533 1 O THR C 530 N LEU C 491 SHEET 1 G 5 VAL D 28 LYS D 32 0 SHEET 2 G 5 ASN D 18 ALA D 22 -1 N VAL D 21 O VAL D 29 SHEET 3 G 5 ASP D 81 GLN D 87 1 O ILE D 83 N LYS D 20 SHEET 4 G 5 ILE D 57 PHE D 61 -1 N ARG D 60 O ASP D 84 SHEET 5 G 5 GLN D 64 PRO D 65 -1 O GLN D 64 N PHE D 61 SHEET 1 H 2 ILE E 388 ALA E 392 0 SHEET 2 H 2 LEU E 395 THR E 398 -1 O ILE E 397 N LEU E 389 SHEET 1 I 2 LEU E 411 ASN E 412 0 SHEET 2 I 2 THR F 90 GLY F 91 -1 O GLY F 91 N LEU E 411 SHEET 1 J 5 LEU E 435 VAL E 437 0 SHEET 2 J 5 ILE E 468 HIS E 474 1 O ILE E 468 N HIS E 436 SHEET 3 J 5 TRP E 479 ASP E 485 -1 O SER E 480 N ILE E 473 SHEET 4 J 5 CYS E 490 LEU E 494 -1 O LEU E 494 N LEU E 481 SHEET 5 J 5 THR E 530 HIS E 532 1 O THR E 530 N LEU E 491 SHEET 1 K 5 VAL F 28 ILE F 33 0 SHEET 2 K 5 ILE F 17 GLY F 23 -1 N VAL F 21 O VAL F 29 SHEET 3 K 5 THR F 82 GLN F 87 1 O ILE F 83 N LYS F 20 SHEET 4 K 5 ILE F 57 PHE F 61 -1 N ARG F 60 O ASP F 84 SHEET 5 K 5 GLN F 64 PRO F 65 -1 O GLN F 64 N PHE F 61 CRYST1 141.980 143.360 134.120 90.00 90.00 90.00 C 2 2 21 24 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 0.007043 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007456 0.00000