HEADER PROTEIN BINDING, HYDROLASE 09-OCT-06 2IO0 TITLE CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 2; COMPND 3 CHAIN: A; 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 2 PRECURSOR; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: SUMO-2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, COMPND 14 SENTRIN-2, HSMT3; 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 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: SUMO2, SMT3B, SMT3H2; 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 2IO0 1 REMARK REVDAT 5 20-OCT-21 2IO0 1 REMARK SEQADV REVDAT 4 18-OCT-17 2IO0 1 REMARK REVDAT 3 24-FEB-09 2IO0 1 VERSN REVDAT 2 02-JAN-07 2IO0 1 JRNL REVDAT 1 14-NOV-06 2IO0 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3134411.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 17291 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) : 0.207 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 875 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2288 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2565 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.89000 REMARK 3 B22 (A**2) : -2.89000 REMARK 3 B33 (A**2) : 5.79000 REMARK 3 B12 (A**2) : 2.12000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 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 : 0.35 REMARK 3 BSOL : 58.43 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 2IO0 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_1000039801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.97950 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 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18192 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 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) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 56.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 0.2M LITHIUM SULFATE, REMARK 280 0.1MM TRIS-HCL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 73.10200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.20546 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.83733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 73.10200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 42.20546 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.83733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 73.10200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 42.20546 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.83733 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 73.10200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 42.20546 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.83733 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 73.10200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 42.20546 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.83733 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 73.10200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 42.20546 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.83733 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 84.41092 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 69.67467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 84.41092 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 69.67467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 84.41092 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 69.67467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 84.41092 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 69.67467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 84.41092 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 69.67467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 84.41092 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 69.67467 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 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 MET B 13 REMARK 465 ALA B 14 REMARK 465 ASN B 15 REMARK 465 HIS B 100 REMARK 465 HIS B 101 REMARK 465 HIS B 102 REMARK 465 HIS B 103 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 541 CG CD OE1 NE2 REMARK 480 GLN A 542 CG CD OE1 NE2 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 A 396 NE - CZ - NH2 ANGL. DEV. = -3.5 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 PRO A 384 107.06 -47.48 REMARK 500 ALA A 392 159.04 178.48 REMARK 500 ARG A 426 -75.96 -59.03 REMARK 500 ASN A 427 -54.24 -27.31 REMARK 500 SER A 448 -76.29 -74.05 REMARK 500 LYS A 488 50.41 -148.60 REMARK 500 LYS A 489 61.95 13.26 REMARK 500 HIS A 502 -67.67 -97.25 REMARK 500 ARG A 503 -72.82 -49.19 REMARK 500 ILE A 504 -64.11 -25.40 REMARK 500 ASN A 525 64.15 -102.31 REMARK 500 LEU A 526 -7.89 -41.80 REMARK 500 HIS A 531 -160.26 -60.64 REMARK 500 HIS A 532 152.19 169.68 REMARK 500 ASP A 562 3.11 83.41 REMARK 500 ILE A 565 96.23 -61.92 REMARK 500 ARG B 36 -14.56 -47.61 REMARK 500 THR B 91 -108.91 -120.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 511 0.07 SIDE CHAIN 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 SO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 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: 2IO1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-3 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 2IO0 A 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO0 B 15 95 UNP P61956 SUMO2_HUMAN 15 95 SEQADV 2IO0 GLY A 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 SER A 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 HIS A 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 MET A 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 ALA A 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 SER A 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO0 SER A 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO0 MET B 13 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 ALA B 14 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 LEU B 96 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 GLU B 97 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 98 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 99 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 100 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 101 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 102 UNP P61956 CLONING ARTIFACT SEQADV 2IO0 HIS B 103 UNP P61956 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 91 MET ALA ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY GLN SEQRES 2 B 91 ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG HIS THR SEQRES 3 B 91 PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU ARG GLN SEQRES 4 B 91 GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE ASP GLY SEQRES 5 B 91 GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN LEU GLU SEQRES 6 B 91 MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN GLN GLN SEQRES 7 B 91 THR GLY GLY VAL TYR LEU GLU HIS HIS HIS HIS HIS HIS HET SO4 A 300 5 HET SO4 A 301 5 HET SO4 B 302 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *129(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 ASN A 412 GLN A 430 1 19 HELIX 5 5 PHE A 441 GLY A 450 1 10 HELIX 6 6 TYR A 451 LYS A 459 5 9 HELIX 7 7 ASN A 462 GLN A 466 5 5 HELIX 8 8 HIS A 502 ASN A 521 1 20 HELIX 9 9 LYS A 535 ILE A 539 5 5 HELIX 10 10 ASN A 544 SER A 546 5 3 HELIX 11 11 ASP A 547 ASP A 562 1 16 HELIX 12 12 THR A 568 HIS A 570 5 3 HELIX 13 13 GLN A 571 GLN A 586 1 16 HELIX 14 14 LEU B 40 GLN B 51 1 12 SHEET 1 A 2 ILE A 388 ALA A 392 0 SHEET 2 A 2 LEU A 395 THR A 398 -1 O LEU A 395 N ALA A 392 SHEET 1 B 4 LEU A 435 VAL A 437 0 SHEET 2 B 4 ILE A 468 HIS A 474 1 O LEU A 470 N HIS A 436 SHEET 3 B 4 TRP A 479 ASP A 485 -1 O VAL A 482 N VAL A 471 SHEET 4 B 4 CYS A 490 LEU A 494 -1 O LEU A 494 N LEU A 481 SHEET 1 C 5 VAL B 29 LYS B 35 0 SHEET 2 C 5 HIS B 17 ALA B 23 -1 N VAL B 22 O VAL B 30 SHEET 3 C 5 ASP B 82 GLN B 88 1 O ILE B 84 N LYS B 21 SHEET 4 C 5 ILE B 58 PHE B 62 -1 N ARG B 61 O ASP B 85 SHEET 5 C 5 GLN B 65 PRO B 66 -1 O GLN B 65 N PHE B 62 SITE 1 AC1 7 HOH A 65 HOH A 76 HOH A 95 ALA A 392 SITE 2 AC1 7 PHE A 393 LYS A 394 ARG A 396 SITE 1 AC2 2 ARG A 475 LYS A 476 SITE 1 AC3 6 ARG A 396 ASN B 68 GLU B 69 THR B 70 SITE 2 AC3 6 HOH B 306 HOH B 333 CRYST1 146.204 146.204 104.512 90.00 90.00 120.00 H 3 2 18 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 0.006840 0.003949 0.000000 0.00000 SCALE2 0.000000 0.007898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009568 0.00000