HEADER PROTEIN BINDING, HYDROLASE 09-OCT-06 2IO2 TITLE CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1-SUMO-1 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 1; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: SUMO-1, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3 HOMOLOG 3, COMPND 14 UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE PROTEIN UBL1, COMPND 15 GAP-MODIFYING PROTEIN 1, GMP1, SENTRIN; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: RAN GTPASE-ACTIVATING PROTEIN 1; COMPND 19 CHAIN: C; COMPND 20 FRAGMENT: C-TERMINAL DOMAIN; COMPND 21 ENGINEERED: YES; COMPND 22 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: SUMO1, SMT3C, SMT3H3, UBL1; 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 20-OCT-21 2IO2 1 SEQADV REVDAT 5 18-OCT-17 2IO2 1 REMARK REVDAT 4 13-JUL-11 2IO2 1 VERSN REVDAT 3 24-FEB-09 2IO2 1 VERSN REVDAT 2 02-JAN-07 2IO2 1 JRNL REVDAT 1 21-NOV-06 2IO2 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. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3563397.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 13579 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) : 0.268 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 676 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2001 REMARK 3 BIN R VALUE (WORKING SET) : 0.4380 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.04000 REMARK 3 B22 (A**2) : 10.04000 REMARK 3 B33 (A**2) : -20.07000 REMARK 3 B12 (A**2) : 14.98000 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) : 0.51 REMARK 3 ESD FROM SIGMAA (A) : 1.12 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) : 0.61 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.94 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 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) : 2.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.22 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 2IO2 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_1000039803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-04 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 : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13707 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 54.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 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 25.92333 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 51.84667 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 25.92333 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 51.84667 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 25.92333 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 51.84667 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 25.92333 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 51.84667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 37350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 75900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -210.0 KCAL/MOL 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 -1.000000 0.000000 0.000000 81.98000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 141.99353 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 25.92333 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 81.98000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 141.99353 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 25.92333 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 MET B 16 REMARK 465 GLY B 17 REMARK 465 GLU B 18 REMARK 465 GLY B 19 REMARK 465 GLU B 20 REMARK 465 TYR B 21 REMARK 465 ILE B 22 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 97 NZ LYS C 524 0.12 REMARK 500 C GLY B 97 NZ LYS C 524 1.33 REMARK 500 OXT GLY B 97 CE LYS C 524 1.56 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 HOH A 2 O HOH A 2 7555 1.12 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 ARG A 475 N - CA - C ANGL. DEV. = -18.9 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 ASP A 386 -16.12 -142.62 REMARK 500 GLU A 387 84.83 -54.11 REMARK 500 ILE A 388 128.76 -39.06 REMARK 500 SER A 390 146.07 -174.74 REMARK 500 ALA A 392 158.62 151.69 REMARK 500 PHE A 393 8.84 57.77 REMARK 500 LYS A 394 21.06 82.23 REMARK 500 TYR A 408 -5.45 65.62 REMARK 500 ASN A 412 -155.61 -78.37 REMARK 500 PHE A 418 -68.68 -94.78 REMARK 500 LYS A 428 -5.67 -143.32 REMARK 500 PHE A 442 -65.28 -100.22 REMARK 500 LYS A 455 -78.85 -41.47 REMARK 500 ARG A 456 0.51 -50.82 REMARK 500 VAL A 461 139.56 -174.60 REMARK 500 ARG A 487 -73.45 -55.17 REMARK 500 GLN A 499 138.29 -39.14 REMARK 500 GLN A 510 -9.61 -55.06 REMARK 500 SER A 516 -76.28 -113.19 REMARK 500 LYS A 517 7.21 -54.90 REMARK 500 ARG A 520 12.68 -174.73 REMARK 500 ASN A 521 -15.80 50.55 REMARK 500 ASP A 523 -160.96 -58.16 REMARK 500 GLU A 538 -71.53 -80.31 REMARK 500 SER A 546 -44.67 -133.63 REMARK 500 TYR A 558 -62.18 -98.60 REMARK 500 ASP A 562 14.91 57.12 REMARK 500 HIS A 570 36.93 -61.99 REMARK 500 GLN A 571 -28.86 -148.57 REMARK 500 PHE A 575 -39.77 -36.78 REMARK 500 VAL B 26 50.18 -144.97 REMARK 500 ASP B 30 -70.33 176.60 REMARK 500 SER B 31 -43.69 177.64 REMARK 500 SER B 32 98.82 -24.68 REMARK 500 LYS B 37 136.69 -170.17 REMARK 500 MET B 40 89.87 -65.14 REMARK 500 THR B 41 -54.92 -173.28 REMARK 500 HIS B 43 158.72 -32.44 REMARK 500 LYS B 48 -73.09 -77.35 REMARK 500 CYS B 52 -0.72 -58.56 REMARK 500 PRO B 58 -175.66 -39.35 REMARK 500 ASN B 60 3.35 -55.33 REMARK 500 ILE B 71 92.14 -51.86 REMARK 500 ALA B 72 177.44 -59.80 REMARK 500 GLU B 85 39.84 72.46 REMARK 500 GLU B 93 156.27 -40.61 REMARK 500 ARG C 448 52.91 -92.54 REMARK 500 LEU C 449 2.70 -150.81 REMARK 500 SER C 454 -76.12 -49.98 REMARK 500 SER C 478 -9.59 -57.84 REMARK 500 REMARK 500 THIS ENTRY HAS 66 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: 2IO3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1-SUMO-2 DBREF 2IO2 A 364 589 UNP Q9HC62 SENP2_HUMAN 364 589 DBREF 2IO2 B 18 97 UNP P63165 SUMO1_HUMAN 18 97 DBREF 2IO2 C 418 587 UNP P46060 RGP1_HUMAN 418 587 SEQADV 2IO2 GLY A 358 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 SER A 359 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 HIS A 360 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 MET A 361 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 ALA A 362 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 SER A 363 UNP Q9HC62 CLONING ARTIFACT SEQADV 2IO2 SER A 548 UNP Q9HC62 CYS 548 ENGINEERED MUTATION SEQADV 2IO2 MET B 16 UNP P63165 CLONING ARTIFACT SEQADV 2IO2 GLY B 17 UNP P63165 CLONING ARTIFACT SEQADV 2IO2 SER C 416 UNP P46060 CLONING ARTIFACT SEQADV 2IO2 LEU C 417 UNP P46060 CLONING ARTIFACT SEQADV 2IO2 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 82 MET GLY GLU GLY GLU TYR ILE LYS LEU LYS VAL ILE GLY SEQRES 2 B 82 GLN ASP SER SER GLU ILE HIS PHE LYS VAL LYS MET THR SEQRES 3 B 82 THR HIS LEU LYS LYS LEU LYS GLU SER TYR CYS GLN ARG SEQRES 4 B 82 GLN GLY VAL PRO MET ASN SER LEU ARG PHE LEU PHE GLU SEQRES 5 B 82 GLY GLN ARG ILE ALA ASP ASN HIS THR PRO LYS GLU LEU SEQRES 6 B 82 GLY MET GLU GLU GLU ASP VAL ILE GLU VAL TYR GLN GLU SEQRES 7 B 82 GLN 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 FORMUL 4 HOH *8(H2 O) HELIX 1 1 THR A 369 GLU A 375 1 7 HELIX 2 2 ILE A 376 GLY A 381 1 6 HELIX 3 3 THR A 398 THR A 404 1 7 HELIX 4 4 ASP A 413 ASN A 427 1 15 HELIX 5 5 PHE A 442 GLY A 450 1 9 HELIX 6 6 TYR A 451 THR A 458 5 8 HELIX 7 7 ASN A 462 GLN A 466 5 5 HELIX 8 8 GLY A 501 THR A 518 1 18 HELIX 9 9 ASP A 547 SER A 560 1 14 HELIX 10 10 THR A 568 HIS A 570 5 3 HELIX 11 11 GLN A 571 GLN A 586 1 16 HELIX 12 12 LEU B 44 CYS B 52 1 9 HELIX 13 13 GLN B 53 GLN B 55 5 3 HELIX 14 14 THR B 76 GLY B 81 1 6 HELIX 15 15 ASP C 433 PHE C 440 1 8 HELIX 16 16 SER C 442 ARG C 448 1 7 HELIX 17 17 LEU C 449 PRO C 451 5 3 HELIX 18 18 LYS C 452 GLN C 460 1 9 HELIX 19 19 ASP C 465 SER C 478 1 14 HELIX 20 20 GLU C 483 ASN C 503 1 21 HELIX 21 21 ASN C 508 MET C 520 1 13 HELIX 22 22 ASP C 527 GLN C 548 1 22 HELIX 23 23 ALA C 554 VAL C 563 1 10 HELIX 24 24 LYS C 565 LEU C 570 1 6 HELIX 25 25 SER C 572 TYR C 585 1 14 SHEET 1 A 2 SER A 390 ALA A 392 0 SHEET 2 A 2 LEU A 395 ILE A 397 -1 O LEU A 395 N ALA A 392 SHEET 1 B 5 LEU A 435 VAL A 437 0 SHEET 2 B 5 ILE A 468 ARG A 475 1 O ILE A 468 N HIS A 436 SHEET 3 B 5 HIS A 478 ASP A 485 -1 O ILE A 484 N ILE A 469 SHEET 4 B 5 CYS A 490 LEU A 494 -1 O LYS A 492 N VAL A 483 SHEET 5 B 5 THR A 530 SER A 533 1 O THR A 530 N LEU A 491 SHEET 1 C 2 LEU B 24 LYS B 25 0 SHEET 2 C 2 ASP B 86 VAL B 87 1 O ASP B 86 N LYS B 25 SHEET 1 D 3 GLN B 69 ARG B 70 0 SHEET 2 D 3 LEU B 62 PHE B 66 -1 N PHE B 66 O GLN B 69 SHEET 3 D 3 VAL B 90 GLN B 92 -1 O TYR B 91 N ARG B 63 CRYST1 163.960 163.960 77.770 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 0.006099 0.003521 0.000000 0.00000 SCALE2 0.000000 0.007043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012858 0.00000 MASTER 429 0 0 25 12 0 0 6 0 0 0 39 END