PDB Short entry for 2IBI HEADER HYDROLASE 11-SEP-06 2IBI TITLE COVALENT UBIQUITIN-USP2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 251-605; COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 2, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 2, DEUBIQUITINATING ENZYME 2, 41 KDA UBIQUITIN-SPECIFIC COMPND 7 PROTEASE; COMPND 8 EC: 3.1.2.15; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN; COMPND 13 CHAIN: B; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP2, UBP41; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RPS27A, UBA52, UBB, UBC; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTBY2 KEYWDS HYDROLASE, PROTEASE, THIOL PROTEASE, UBL CONJUGATION PATHWAY, KEYWDS 2 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WALKER,G.V.AVVAKUMOV,G.BERNSTEIN,S.XUE,P.J.FINERTY JR., AUTHOR 2 F.MACKENZIE,J.WEIGELT,M.SUNDSTROM,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 3 A.BOCHKAREV,S.DHE-PAGANON,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 30-AUG-23 2IBI 1 REMARK REVDAT 3 20-OCT-21 2IBI 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2IBI 1 VERSN REVDAT 1 24-OCT-06 2IBI 0 JRNL AUTH G.V.AVVAKUMOV,J.R.WALKER,G.BERNSTEIN,S.XUE,P.J.FINERTY JR., JRNL AUTH 2 F.MACKENZIE,J.WEIGELT,M.SUNDSTROM,C.H.ARROWSMITH, JRNL AUTH 3 A.M.EDWARDS,A.BOCHKAREV,S.DHE-PAGANON JRNL TITL COVALENT UBIQUITIN-USP2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 18491 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 + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 996 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3299 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : 0.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.363 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.253 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.208 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.288 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3388 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4568 ; 1.399 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 409 ; 6.696 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;32.189 ;23.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 607 ;17.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;20.757 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 504 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2559 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1458 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2243 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 183 ; 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 43 ; 0.216 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.242 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2102 ; 1.757 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3319 ; 2.839 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1427 ; 3.580 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1249 ; 5.310 ; 7.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19694 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.65000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 2GFO, 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG1500, 0.1 M BICINE, 0.2 M NACL, REMARK 280 1 MM DTT, PH 9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, REMARK 280 PH 9.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.41950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.41950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.20000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 MET A 232 REMARK 465 GLY A 233 REMARK 465 SER A 234 REMARK 465 SER A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 SER A 242 REMARK 465 SER A 243 REMARK 465 GLY A 244 REMARK 465 LEU A 245 REMARK 465 VAL A 246 REMARK 465 PRO A 247 REMARK 465 ARG A 248 REMARK 465 GLY A 249 REMARK 465 SER A 250 REMARK 465 SER A 251 REMARK 465 SER A 252 REMARK 465 PRO A 253 REMARK 465 GLY A 254 REMARK 465 ARG A 255 REMARK 465 ASP A 256 REMARK 465 GLY A 257 REMARK 465 MET A 258 REMARK 465 ASN A 259 REMARK 465 SER A 260 REMARK 465 LYS A 261 REMARK 465 SER A 262 REMARK 465 SER A 382 REMARK 465 TYR A 450 REMARK 465 ASN A 537 REMARK 465 PRO A 601 REMARK 465 PRO A 602 REMARK 465 SER A 603 REMARK 465 ARG A 604 REMARK 465 MET A 605 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 CA GLY B 75 N NEH B 76 2.14 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 B 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 72 NE - CZ - NH1 ANGL. DEV. = 3.1 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 266 44.67 -102.14 REMARK 500 ASP A 408 89.78 -153.27 REMARK 500 ARG A 448 101.46 -52.27 REMARK 500 ARG A 504 49.92 -88.72 REMARK 500 SER A 508 132.38 -26.22 REMARK 500 GLU A 534 80.23 -166.85 REMARK 500 ASP A 575 -119.81 52.91 REMARK 500 THR B 7 -159.72 -83.48 REMARK 500 LYS B 63 127.74 -35.34 REMARK 500 LEU B 71 -143.47 -101.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 425 SG REMARK 620 2 CYS A 428 SG 111.1 REMARK 620 3 CYS A 476 SG 110.1 105.6 REMARK 620 4 CYS A 479 SG 110.7 107.6 111.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NEH B 76 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HD5 RELATED DB: PDB REMARK 900 USP2 IN COMPLEX WITH UBIQUITIN DBREF 2IBI A 251 605 UNP O75604 UBP2_HUMAN 250 605 DBREF 2IBI B 1 75 UNP P62988 UBIQ_HUMAN 1 75 SEQADV 2IBI MET A 232 UNP O75604 INITIATING METHIONINE SEQADV 2IBI GLY A 233 UNP O75604 CLONING ARTIFACT SEQADV 2IBI SER A 234 UNP O75604 CLONING ARTIFACT SEQADV 2IBI SER A 235 UNP O75604 CLONING ARTIFACT SEQADV 2IBI HIS A 236 UNP O75604 EXPRESSION TAG SEQADV 2IBI HIS A 237 UNP O75604 EXPRESSION TAG SEQADV 2IBI HIS A 238 UNP O75604 EXPRESSION TAG SEQADV 2IBI HIS A 239 UNP O75604 EXPRESSION TAG SEQADV 2IBI HIS A 240 UNP O75604 EXPRESSION TAG SEQADV 2IBI HIS A 241 UNP O75604 EXPRESSION TAG SEQADV 2IBI SER A 242 UNP O75604 CLONING ARTIFACT SEQADV 2IBI SER A 243 UNP O75604 CLONING ARTIFACT SEQADV 2IBI GLY A 244 UNP O75604 CLONING ARTIFACT SEQADV 2IBI LEU A 245 UNP O75604 CLONING ARTIFACT SEQADV 2IBI VAL A 246 UNP O75604 CLONING ARTIFACT SEQADV 2IBI PRO A 247 UNP O75604 CLONING ARTIFACT SEQADV 2IBI ARG A 248 UNP O75604 CLONING ARTIFACT SEQADV 2IBI GLY A 249 UNP O75604 CLONING ARTIFACT SEQADV 2IBI SER A 250 UNP O75604 CLONING ARTIFACT SEQADV 2IBI ALA A 472 UNP O75604 GLU 472 ENGINEERED MUTATION SEQADV 2IBI ALA A 473 UNP O75604 LYS 473 ENGINEERED MUTATION SEQRES 1 A 374 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 374 LEU VAL PRO ARG GLY SER SER SER PRO GLY ARG ASP GLY SEQRES 3 A 374 MET ASN SER LYS SER ALA GLN GLY LEU ALA GLY LEU ARG SEQRES 4 A 374 ASN LEU GLY ASN THR CYS PHE MET ASN SER ILE LEU GLN SEQRES 5 A 374 CYS LEU SER ASN THR ARG GLU LEU ARG ASP TYR CYS LEU SEQRES 6 A 374 GLN ARG LEU TYR MET ARG ASP LEU HIS HIS GLY SER ASN SEQRES 7 A 374 ALA HIS THR ALA LEU VAL GLU GLU PHE ALA LYS LEU ILE SEQRES 8 A 374 GLN THR ILE TRP THR SER SER PRO ASN ASP VAL VAL SER SEQRES 9 A 374 PRO SER GLU PHE LYS THR GLN ILE GLN ARG TYR ALA PRO SEQRES 10 A 374 ARG PHE VAL GLY TYR ASN GLN GLN ASP ALA GLN GLU PHE SEQRES 11 A 374 LEU ARG PHE LEU LEU ASP GLY LEU HIS ASN GLU VAL ASN SEQRES 12 A 374 ARG VAL THR LEU ARG PRO LYS SER ASN PRO GLU ASN LEU SEQRES 13 A 374 ASP HIS LEU PRO ASP ASP GLU LYS GLY ARG GLN MET TRP SEQRES 14 A 374 ARG LYS TYR LEU GLU ARG GLU ASP SER ARG ILE GLY ASP SEQRES 15 A 374 LEU PHE VAL GLY GLN LEU LYS SER SER LEU THR CYS THR SEQRES 16 A 374 ASP CYS GLY TYR CYS SER THR VAL PHE ASP PRO PHE TRP SEQRES 17 A 374 ASP LEU SER LEU PRO ILE ALA LYS ARG GLY TYR PRO GLU SEQRES 18 A 374 VAL THR LEU MET ASP CYS MET ARG LEU PHE THR LYS GLU SEQRES 19 A 374 ASP VAL LEU ASP GLY ASP ALA ALA PRO THR CYS CYS ARG SEQRES 20 A 374 CYS ARG GLY ARG LYS ARG CYS ILE LYS LYS PHE SER ILE SEQRES 21 A 374 GLN ARG PHE PRO LYS ILE LEU VAL LEU HIS LEU LYS ARG SEQRES 22 A 374 PHE SER GLU SER ARG ILE ARG THR SER LYS LEU THR THR SEQRES 23 A 374 PHE VAL ASN PHE PRO LEU ARG ASP LEU ASP LEU ARG GLU SEQRES 24 A 374 PHE ALA SER GLU ASN THR ASN HIS ALA VAL TYR ASN LEU SEQRES 25 A 374 TYR ALA VAL SER ASN HIS SER GLY THR THR MET GLY GLY SEQRES 26 A 374 HIS TYR THR ALA TYR CYS ARG SER PRO GLY THR GLY GLU SEQRES 27 A 374 TRP HIS THR PHE ASN ASP SER SER VAL THR PRO MET SER SEQRES 28 A 374 SER SER GLN VAL ARG THR SER ASP ALA TYR LEU LEU PHE SEQRES 29 A 374 TYR GLU LEU ALA SER PRO PRO SER ARG MET SEQRES 1 B 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY HET ZN A 1 1 HET NEH B 76 3 HETNAM ZN ZINC ION HETNAM NEH ETHANAMINE FORMUL 3 ZN ZN 2+ FORMUL 4 NEH C2 H7 N FORMUL 5 HOH *100(H2 O) HELIX 1 1 THR A 275 ASN A 287 1 13 HELIX 2 2 THR A 288 GLN A 297 1 10 HELIX 3 3 LEU A 299 LEU A 304 1 6 HELIX 4 4 HIS A 311 THR A 327 1 17 HELIX 5 5 PRO A 336 ALA A 347 1 12 HELIX 6 6 PRO A 348 VAL A 351 5 4 HELIX 7 7 ASP A 357 VAL A 373 1 17 HELIX 8 8 PRO A 391 GLU A 405 1 15 HELIX 9 9 SER A 409 VAL A 416 1 8 HELIX 10 10 LEU A 455 THR A 463 1 9 HELIX 11 11 ASP A 469 ALA A 473 5 5 HELIX 12 12 ARG A 529 ALA A 532 5 4 HELIX 13 13 SER A 582 VAL A 586 5 5 HELIX 14 14 THR B 22 GLY B 35 1 14 HELIX 15 15 PRO B 37 GLN B 41 5 5 SHEET 1 A 2 GLY A 268 LEU A 269 0 SHEET 2 A 2 VAL A 333 VAL A 334 1 O VAL A 334 N GLY A 268 SHEET 1 B 4 CYS A 431 PHE A 438 0 SHEET 2 B 4 GLY A 417 CYS A 425 -1 N LEU A 419 O ASP A 436 SHEET 3 B 4 CYS A 485 ARG A 493 -1 O SER A 490 N LYS A 420 SHEET 4 B 4 ASP A 466 LEU A 468 -1 N ASP A 466 O LYS A 487 SHEET 1 C 5 LEU A 441 LEU A 443 0 SHEET 2 C 5 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 C 5 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 C 5 VAL A 540 GLY A 551 -1 N ALA A 545 O PHE A 595 SHEET 5 C 5 LEU A 526 ASP A 527 -1 N LEU A 526 O TYR A 541 SHEET 1 D 7 LEU A 441 LEU A 443 0 SHEET 2 D 7 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 D 7 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 D 7 VAL A 540 GLY A 551 -1 N ALA A 545 O PHE A 595 SHEET 5 D 7 GLY A 556 ARG A 563 -1 O ARG A 563 N TYR A 544 SHEET 6 D 7 TRP A 570 ASN A 574 -1 O PHE A 573 N ALA A 560 SHEET 7 D 7 SER A 577 MET A 581 -1 O SER A 577 N ASN A 574 SHEET 1 E 2 VAL A 453 THR A 454 0 SHEET 2 E 2 VAL A 519 ASN A 520 1 O ASN A 520 N VAL A 453 SHEET 1 F 2 THR A 475 CYS A 476 0 SHEET 2 F 2 GLY A 481 ARG A 482 -1 O GLY A 481 N CYS A 476 SHEET 1 G 5 THR B 12 GLU B 16 0 SHEET 2 G 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 G 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 G 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 G 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS A 276 CB NEH B 76 1555 1555 1.82 LINK C GLY B 75 N NEH B 76 1555 1555 1.27 LINK ZN ZN A 1 SG CYS A 425 1555 1555 2.36 LINK ZN ZN A 1 SG CYS A 428 1555 1555 2.32 LINK ZN ZN A 1 SG CYS A 476 1555 1555 2.27 LINK ZN ZN A 1 SG CYS A 479 1555 1555 2.38 SITE 1 AC1 4 CYS A 425 CYS A 428 CYS A 476 CYS A 479 SITE 1 AC2 6 ASN A 274 CYS A 276 GLN A 355 GLY A 556 SITE 2 AC2 6 HIS A 557 GLY B 75 CRYST1 102.839 54.400 75.021 90.00 107.66 90.00 C 1 2 1 4 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 0.009724 0.000000 0.003096 0.00000 SCALE2 0.000000 0.018382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013989 0.00000