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