HEADER PROTEIN BINDING, HYDROLASE 09-OCT-06 2IO3 TITLE CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1-SUMO-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; 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; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: RAN GTPASE-ACTIVATING PROTEIN 1; COMPND 18 CHAIN: C; COMPND 19 FRAGMENT: C-TERMINAL DOMAIN; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: 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; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: RANGAP1; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 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 2IO3 1 REMARK REVDAT 5 20-OCT-21 2IO3 1 SEQADV REVDAT 4 18-OCT-17 2IO3 1 REMARK REVDAT 3 24-FEB-09 2IO3 1 VERSN REVDAT 2 02-JAN-07 2IO3 1 JRNL REVDAT 1 14-NOV-06 2IO3 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. 3.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3583109.490 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 10451 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) : 0.277 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 529 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1597 REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 92 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3664 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 92.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 23.31000 REMARK 3 B22 (A**2) : 23.31000 REMARK 3 B33 (A**2) : -46.61000 REMARK 3 B12 (A**2) : 29.46000 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) : 0.49 REMARK 3 ESD FROM SIGMAA (A) : 0.77 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) : 0.57 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 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 : 0.19 REMARK 3 BSOL : 10.00 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 2IO3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-05 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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10000 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 : 10581 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.3000 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) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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 (%): 55.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 4000, 0.1M LITHIUM CHLORIDE, REMARK 280 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 26.03133 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 52.06267 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.03133 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 52.06267 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.03133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 52.06267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 26.03133 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.06267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 THERE IS A DOMAIN-SWAPPED DIMER ACROSS CRYSTALLOGRAPHIC REMARK 300 TWO-FOLD INVOLVING CHAIN C, FORMED BY SYMMETRY OPERATION REMARK 300 7555 (Y,X,1/3-Z) 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.03133 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 82.02800 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 142.07666 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 82.02800 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 142.07666 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 26.03133 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 MET B 13 REMARK 465 ALA B 14 REMARK 465 ASN B 15 REMARK 465 ASP B 16 REMARK 465 HIS B 17 REMARK 465 ILE B 18 REMARK 465 ASN B 19 REMARK 465 SER C 416 REMARK 465 LEU C 417 REMARK 465 ASN C 418 REMARK 465 THR C 419 REMARK 465 GLY C 420 REMARK 465 GLU C 421 REMARK 465 PRO C 422 REMARK 465 ALA C 423 REMARK 465 PRO C 424 REMARK 465 VAL C 425 REMARK 465 LEU C 426 REMARK 465 SER C 427 REMARK 465 SER C 428 REMARK 465 PRO C 429 REMARK 465 PRO C 430 REMARK 465 PRO C 431 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 OXT GLY B 93 NZ LYS C 524 0.13 REMARK 500 C GLY B 93 NZ LYS C 524 1.33 REMARK 500 OXT GLY B 93 CE LYS C 524 1.58 REMARK 500 O LEU B 43 CD1 TYR B 47 2.14 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 B 56 O PRO C 441 7555 2.07 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 PHE B 32 CB - CA - C ANGL. DEV. = -12.5 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 LEU A 368 43.56 -163.47 REMARK 500 THR A 369 99.31 -45.60 REMARK 500 LYS A 374 23.23 -78.63 REMARK 500 ILE A 376 -62.86 -94.27 REMARK 500 LEU A 389 20.18 -150.06 REMARK 500 SER A 390 167.43 176.27 REMARK 500 ALA A 392 163.61 166.28 REMARK 500 PHE A 393 34.07 32.67 REMARK 500 ARG A 399 0.42 -64.09 REMARK 500 TYR A 408 -9.91 64.06 REMARK 500 ASN A 412 -159.88 -91.83 REMARK 500 PHE A 418 -61.15 -97.27 REMARK 500 ALA A 434 100.18 -54.60 REMARK 500 GLN A 452 -38.76 -39.43 REMARK 500 LYS A 455 -80.27 -42.00 REMARK 500 VAL A 461 138.34 -175.04 REMARK 500 PHE A 464 -13.54 -48.80 REMARK 500 PRO A 472 98.07 -69.04 REMARK 500 LYS A 476 123.45 -11.65 REMARK 500 VAL A 477 -4.43 73.21 REMARK 500 GLN A 499 156.95 -45.20 REMARK 500 THR A 518 54.98 -111.50 REMARK 500 LYS A 519 -3.47 -170.38 REMARK 500 ARG A 520 10.17 -154.13 REMARK 500 ASN A 521 6.51 52.09 REMARK 500 ASP A 523 -141.28 -73.09 REMARK 500 LEU A 524 109.94 -162.77 REMARK 500 HIS A 532 166.06 164.76 REMARK 500 LYS A 535 131.09 -38.90 REMARK 500 GLU A 538 -88.95 -86.93 REMARK 500 ASN A 544 -146.84 -157.18 REMARK 500 ASP A 547 34.32 -76.23 REMARK 500 ALA A 556 -2.35 -55.27 REMARK 500 ASP A 557 -69.34 -107.36 REMARK 500 ASP A 562 28.72 40.36 REMARK 500 ILE A 565 98.89 -69.34 REMARK 500 MET A 572 -56.15 -27.06 REMARK 500 VAL B 29 80.12 -171.29 REMARK 500 PHE B 32 -152.82 -157.25 REMARK 500 ARG B 36 -88.49 -58.63 REMARK 500 HIS B 37 23.30 -68.76 REMARK 500 ARG B 50 7.55 -62.45 REMARK 500 GLN B 51 -13.72 -150.80 REMARK 500 ASP B 63 13.04 55.34 REMARK 500 GLU B 69 -70.03 -60.97 REMARK 500 THR B 70 -2.11 -57.34 REMARK 500 GLN B 75 -70.68 -49.81 REMARK 500 LEU B 76 11.38 -56.74 REMARK 500 GLU B 77 79.36 35.22 REMARK 500 GLU B 79 -164.86 -118.10 REMARK 500 REMARK 500 THIS ENTRY HAS 76 RAMACHANDRAN OUTLIERS. 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: 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 DBREF 2IO3 A 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO3 B 15 93 UNP P61956 SUMO2_HUMAN 15 93 DBREF 2IO3 C 418 587 UNP P46060 RGP1_HUMAN 418 587 SEQADV 2IO3 GLY A 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 SER A 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 HIS A 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 MET A 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 ALA A 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 SER A 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO3 SER A 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO3 MET B 13 UNP P61956 CLONING ARTIFACT SEQADV 2IO3 ALA B 14 UNP P61956 CLONING ARTIFACT SEQADV 2IO3 SER C 416 UNP P46060 CLONING ARTIFACT SEQADV 2IO3 LEU C 417 UNP P46060 CLONING ARTIFACT SEQADV 2IO3 SER C 573 UNP P46060 CYS 573 ENGINEERED MUTATION 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 81 MET ALA ASN ASP HIS ILE ASN LEU LYS VAL ALA GLY GLN SEQRES 2 B 81 ASP GLY SER VAL VAL GLN PHE LYS ILE LYS ARG HIS THR SEQRES 3 B 81 PRO LEU SER LYS LEU MET LYS ALA TYR CYS GLU ARG GLN SEQRES 4 B 81 GLY LEU SER MET ARG GLN ILE ARG PHE ARG PHE ASP GLY SEQRES 5 B 81 GLN PRO ILE ASN GLU THR ASP THR PRO ALA GLN LEU GLU SEQRES 6 B 81 MET GLU ASP GLU ASP THR ILE ASP VAL PHE GLN GLN GLN SEQRES 7 B 81 THR GLY GLY SEQRES 1 C 172 SER LEU ASN THR GLY GLU PRO ALA PRO VAL LEU SER SER SEQRES 2 C 172 PRO PRO PRO ALA ASP VAL SER THR PHE LEU ALA PHE PRO SEQRES 3 C 172 SER PRO GLU LYS LEU LEU ARG LEU GLY PRO LYS SER SER SEQRES 4 C 172 VAL LEU ILE ALA GLN GLN THR ASP THR SER ASP PRO GLU SEQRES 5 C 172 LYS VAL VAL SER ALA PHE LEU LYS VAL SER SER VAL PHE SEQRES 6 C 172 LYS ASP GLU ALA THR VAL ARG MET ALA VAL GLN ASP ALA SEQRES 7 C 172 VAL ASP ALA LEU MET GLN LYS ALA PHE ASN SER SER SER SEQRES 8 C 172 PHE ASN SER ASN THR PHE LEU THR ARG LEU LEU VAL HIS SEQRES 9 C 172 MET GLY LEU LEU LYS SER GLU ASP LYS VAL LYS ALA ILE SEQRES 10 C 172 ALA ASN LEU TYR GLY PRO LEU MET ALA LEU ASN HIS MET SEQRES 11 C 172 VAL GLN GLN ASP TYR PHE PRO LYS ALA LEU ALA PRO LEU SEQRES 12 C 172 LEU LEU ALA PHE VAL THR LYS PRO ASN SER ALA LEU GLU SEQRES 13 C 172 SER SER SER PHE ALA ARG HIS SER LEU LEU GLN THR LEU SEQRES 14 C 172 TYR LYS VAL HELIX 1 1 THR A 369 LYS A 374 1 6 HELIX 2 2 ASP A 401 LYS A 406 5 6 HELIX 3 3 ASN A 412 MET A 420 1 9 HELIX 4 4 ASN A 421 GLN A 430 1 10 HELIX 5 5 PHE A 441 GLY A 450 1 10 HELIX 6 6 VAL A 454 LYS A 459 5 6 HELIX 7 7 HIS A 502 ASN A 521 1 20 HELIX 8 8 ASN A 525 TRP A 529 5 5 HELIX 9 9 ASP A 547 ILE A 559 1 13 HELIX 10 10 GLN A 571 HIS A 585 1 15 HELIX 11 11 LEU B 40 ARG B 50 1 11 HELIX 12 12 ALA C 432 PHE C 440 1 9 HELIX 13 13 SER C 442 ARG C 448 1 7 HELIX 14 14 LEU C 449 PRO C 451 5 3 HELIX 15 15 LYS C 452 GLN C 460 1 9 HELIX 16 16 PRO C 466 SER C 478 1 13 HELIX 17 17 GLU C 483 ASN C 503 1 21 HELIX 18 18 ASN C 508 LEU C 517 1 10 HELIX 19 19 ASP C 527 GLY C 537 1 11 HELIX 20 20 GLY C 537 VAL C 546 1 10 HELIX 21 21 LEU C 555 ALA C 561 1 7 HELIX 22 22 LYS C 565 LEU C 570 1 6 HELIX 23 23 SER C 572 TYR C 585 1 14 SHEET 1 A 5 LEU A 435 VAL A 437 0 SHEET 2 A 5 ILE A 468 ARG A 475 1 O ILE A 468 N HIS A 436 SHEET 3 A 5 HIS A 478 ASP A 485 -1 O SER A 480 N ILE A 473 SHEET 4 A 5 CYS A 490 LEU A 494 -1 O LEU A 494 N LEU A 481 SHEET 5 A 5 THR A 530 HIS A 532 1 O HIS A 532 N TYR A 493 SHEET 1 B 4 VAL B 30 GLN B 31 0 SHEET 2 B 4 LYS B 21 ALA B 23 -1 N VAL B 22 O VAL B 30 SHEET 3 B 4 THR B 83 GLN B 88 1 O ILE B 84 N LYS B 21 SHEET 4 B 4 ILE B 58 ARG B 61 -1 N ARG B 59 O PHE B 87 CRYST1 164.056 164.056 78.094 90.00 90.00 120.00 P 64 2 2 12 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 0.006095 0.003519 0.000000 0.00000 SCALE2 0.000000 0.007038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012805 0.00000