HEADER HYDROLASE 18-OCT-14 4WPH TITLE CRYSTAL STRUCTURE OF USP7 UBIQUITIN-LIKE DOMAINS IN COMPACT TITLE 2 CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN (UNP RESIDUES 535-888); COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 6 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- COMPND 7 PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: ICP0; COMPND 12 CHAIN: C, D; COMPND 13 FRAGMENT: USP7 BINDING SEQUENCE; 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: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15TV-L; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17); SOURCE 14 ORGANISM_TAXID: 10299 KEYWDS DEUBIQUITINATING (DUB) ENZYME, UBIQUITIN-LIKE (UBL) DOMAINS, ICP0 KEYWDS 2 BINDING SITE, HAUSP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.PFOH,I.LACDAO,V.SARIDAKIS REVDAT 4 27-DEC-23 4WPH 1 REMARK REVDAT 3 08-JAN-20 4WPH 1 REMARK REVDAT 2 27-SEP-17 4WPH 1 SOURCE REMARK REVDAT 1 17-JUN-15 4WPH 0 JRNL AUTH R.PFOH,I.K.LACDAO,A.A.GEORGES,A.CAPAR,H.ZHENG,L.FRAPPIER, JRNL AUTH 2 V.SARIDAKIS JRNL TITL CRYSTAL STRUCTURE OF USP7 UBIQUITIN-LIKE DOMAINS WITH AN JRNL TITL 2 ICP0 PEPTIDE REVEALS A NOVEL MECHANISM USED BY VIRAL AND JRNL TITL 3 CELLULAR PROTEINS TO TARGET USP7. JRNL REF PLOS PATHOG. V. 11 04950 2015 JRNL REFN ESSN 1553-7374 JRNL PMID 26046769 JRNL DOI 10.1371/JOURNAL.PPAT.1004950 REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19939 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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) : 2.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1447 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.4240 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5519 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 1.34000 REMARK 3 B12 (A**2) : -0.41000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.412 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.319 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.065 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5653 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5376 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7627 ; 1.290 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12372 ; 0.856 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 677 ; 6.037 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;38.086 ;24.371 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1030 ;16.954 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.309 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6362 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1300 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 543 880 B 543 880 18948 0.090 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 540 A 2120 REMARK 3 RESIDUE RANGE : D 618 D 626 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7260 -0.3920 -25.2290 REMARK 3 T TENSOR REMARK 3 T11: 0.2999 T22: 0.3126 REMARK 3 T33: 0.0893 T12: 0.2224 REMARK 3 T13: 0.1079 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 0.0475 L22: 0.7903 REMARK 3 L33: 0.5052 L12: 0.0692 REMARK 3 L13: 0.0990 L23: 0.0650 REMARK 3 S TENSOR REMARK 3 S11: -0.0271 S12: -0.0461 S13: 0.0203 REMARK 3 S21: -0.1228 S22: -0.0411 S23: -0.1482 REMARK 3 S31: -0.0455 S32: 0.0887 S33: 0.0682 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 543 B 2117 REMARK 3 RESIDUE RANGE : C 617 C 626 REMARK 3 ORIGIN FOR THE GROUP (A): 21.8980 -26.1180 -8.6170 REMARK 3 T TENSOR REMARK 3 T11: 0.4292 T22: 0.3513 REMARK 3 T33: 0.0380 T12: 0.2990 REMARK 3 T13: 0.1001 T23: 0.1111 REMARK 3 L TENSOR REMARK 3 L11: 0.6013 L22: 0.3621 REMARK 3 L33: 0.0862 L12: 0.0638 REMARK 3 L13: 0.1712 L23: -0.0930 REMARK 3 S TENSOR REMARK 3 S11: 0.1261 S12: -0.0980 S13: -0.0311 REMARK 3 S21: -0.0489 S22: -0.1196 S23: -0.0085 REMARK 3 S31: 0.0351 S32: 0.0032 S33: -0.0064 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 : 1.20 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4WPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000202912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.920 REMARK 200 RESOLUTION RANGE LOW (A) : 30.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 1.860 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, SODIUM CITRATE, L-PROLINE, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -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 126.85533 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 63.42767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.42767 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 126.85533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 REMARK 350 BIOMOLECULE: 2 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 514 REMARK 465 GLY A 515 REMARK 465 SER A 516 REMARK 465 SER A 517 REMARK 465 HIS A 518 REMARK 465 HIS A 519 REMARK 465 HIS A 520 REMARK 465 HIS A 521 REMARK 465 HIS A 522 REMARK 465 HIS A 523 REMARK 465 SER A 524 REMARK 465 SER A 525 REMARK 465 GLY A 526 REMARK 465 ARG A 527 REMARK 465 GLU A 528 REMARK 465 ASN A 529 REMARK 465 LEU A 530 REMARK 465 TYR A 531 REMARK 465 PHE A 532 REMARK 465 GLN A 533 REMARK 465 GLY A 534 REMARK 465 ASP A 535 REMARK 465 ILE A 536 REMARK 465 PRO A 537 REMARK 465 GLN A 538 REMARK 465 GLN A 539 REMARK 465 ASP A 639 REMARK 465 ASN A 640 REMARK 465 GLU A 641 REMARK 465 ALA A 642 REMARK 465 ASP A 643 REMARK 465 GLY A 644 REMARK 465 ASN A 645 REMARK 465 GLY A 844 REMARK 465 TYR A 845 REMARK 465 THR A 886 REMARK 465 ASP A 887 REMARK 465 PHE A 888 REMARK 465 MET B 514 REMARK 465 GLY B 515 REMARK 465 SER B 516 REMARK 465 SER B 517 REMARK 465 HIS B 518 REMARK 465 HIS B 519 REMARK 465 HIS B 520 REMARK 465 HIS B 521 REMARK 465 HIS B 522 REMARK 465 HIS B 523 REMARK 465 SER B 524 REMARK 465 SER B 525 REMARK 465 GLY B 526 REMARK 465 ARG B 527 REMARK 465 GLU B 528 REMARK 465 ASN B 529 REMARK 465 LEU B 530 REMARK 465 TYR B 531 REMARK 465 PHE B 532 REMARK 465 GLN B 533 REMARK 465 GLY B 534 REMARK 465 ASP B 535 REMARK 465 ILE B 536 REMARK 465 PRO B 537 REMARK 465 GLN B 538 REMARK 465 GLN B 539 REMARK 465 LEU B 540 REMARK 465 VAL B 541 REMARK 465 GLU B 542 REMARK 465 ASP B 639 REMARK 465 ASN B 640 REMARK 465 GLU B 641 REMARK 465 ALA B 642 REMARK 465 ASP B 643 REMARK 465 GLY B 644 REMARK 465 ASN B 645 REMARK 465 THR B 802 REMARK 465 ILE B 803 REMARK 465 PRO B 804 REMARK 465 ASN B 805 REMARK 465 GLY B 844 REMARK 465 TYR B 845 REMARK 465 LYS B 882 REMARK 465 MET B 883 REMARK 465 LYS B 884 REMARK 465 ILE B 885 REMARK 465 THR B 886 REMARK 465 ASP B 887 REMARK 465 PHE B 888 REMARK 465 HIS C 627 REMARK 465 GLY D 617 REMARK 465 HIS D 627 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 543 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 546 CG CD OE1 OE2 REMARK 470 GLU A 547 CG CD OE1 OE2 REMARK 470 ILE A 550 CG1 CG2 CD1 REMARK 470 GLU A 551 CG CD OE1 OE2 REMARK 470 ALA A 552 CB REMARK 470 GLN A 553 CG CD OE1 NE2 REMARK 470 LYS A 554 CG CD CE NZ REMARK 470 GLU A 668 CG CD OE1 OE2 REMARK 470 ALA A 671 CB REMARK 470 PHE A 867 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 883 CG SD CE REMARK 470 ARG B 543 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 544 CG CD1 CD2 REMARK 470 GLN B 545 CG CD OE1 NE2 REMARK 470 GLU B 546 CG CD OE1 OE2 REMARK 470 GLN B 553 CG CD OE1 NE2 REMARK 470 LYS B 556 CG CD CE NZ REMARK 470 GLU B 668 CG CD OE1 OE2 REMARK 470 CYS B 799 SG REMARK 470 SER B 842 OG REMARK 470 ARG B 846 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 869 CG CD CE NZ REMARK 470 PRO B 870 CG CD REMARK 470 ARG B 871 CG CD NE CZ NH1 NH2 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 OG SER A 752 OD1 ASP A 754 2.18 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 582 -158.44 58.12 REMARK 500 ASN A 656 109.23 -168.38 REMARK 500 ASP A 771 63.78 -104.30 REMARK 500 ASP B 582 -156.61 58.79 REMARK 500 ASN B 656 107.80 -169.91 REMARK 500 LYS B 770 153.46 -47.38 REMARK 500 THR D 625 34.84 -148.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WPI RELATED DB: PDB DBREF 4WPH A 535 888 UNP Q93009 UBP7_HUMAN 535 888 DBREF 4WPH B 535 888 UNP Q93009 UBP7_HUMAN 535 888 DBREF 4WPH C 617 627 PDB 4WPH 4WPH 617 627 DBREF 4WPH D 617 627 PDB 4WPH 4WPH 617 627 SEQADV 4WPH MET A 514 UNP Q93009 INITIATING METHIONINE SEQADV 4WPH GLY A 515 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER A 516 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER A 517 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 518 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 519 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 520 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 521 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 522 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS A 523 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER A 524 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER A 525 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLY A 526 UNP Q93009 EXPRESSION TAG SEQADV 4WPH ARG A 527 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLU A 528 UNP Q93009 EXPRESSION TAG SEQADV 4WPH ASN A 529 UNP Q93009 EXPRESSION TAG SEQADV 4WPH LEU A 530 UNP Q93009 EXPRESSION TAG SEQADV 4WPH TYR A 531 UNP Q93009 EXPRESSION TAG SEQADV 4WPH PHE A 532 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLN A 533 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLY A 534 UNP Q93009 EXPRESSION TAG SEQADV 4WPH MET B 514 UNP Q93009 INITIATING METHIONINE SEQADV 4WPH GLY B 515 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER B 516 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER B 517 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 518 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 519 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 520 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 521 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 522 UNP Q93009 EXPRESSION TAG SEQADV 4WPH HIS B 523 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER B 524 UNP Q93009 EXPRESSION TAG SEQADV 4WPH SER B 525 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLY B 526 UNP Q93009 EXPRESSION TAG SEQADV 4WPH ARG B 527 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLU B 528 UNP Q93009 EXPRESSION TAG SEQADV 4WPH ASN B 529 UNP Q93009 EXPRESSION TAG SEQADV 4WPH LEU B 530 UNP Q93009 EXPRESSION TAG SEQADV 4WPH TYR B 531 UNP Q93009 EXPRESSION TAG SEQADV 4WPH PHE B 532 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLN B 533 UNP Q93009 EXPRESSION TAG SEQADV 4WPH GLY B 534 UNP Q93009 EXPRESSION TAG SEQRES 1 A 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 375 ARG GLU ASN LEU TYR PHE GLN GLY ASP ILE PRO GLN GLN SEQRES 3 A 375 LEU VAL GLU ARG LEU GLN GLU GLU LYS ARG ILE GLU ALA SEQRES 4 A 375 GLN LYS ARG LYS GLU ARG GLN GLU ALA HIS LEU TYR MET SEQRES 5 A 375 GLN VAL GLN ILE VAL ALA GLU ASP GLN PHE CYS GLY HIS SEQRES 6 A 375 GLN GLY ASN ASP MET TYR ASP GLU GLU LYS VAL LYS TYR SEQRES 7 A 375 THR VAL PHE LYS VAL LEU LYS ASN SER SER LEU ALA GLU SEQRES 8 A 375 PHE VAL GLN SER LEU SER GLN THR MET GLY PHE PRO GLN SEQRES 9 A 375 ASP GLN ILE ARG LEU TRP PRO MET GLN ALA ARG SER ASN SEQRES 10 A 375 GLY THR LYS ARG PRO ALA MET LEU ASP ASN GLU ALA ASP SEQRES 11 A 375 GLY ASN LYS THR MET ILE GLU LEU SER ASP ASN GLU ASN SEQRES 12 A 375 PRO TRP THR ILE PHE LEU GLU THR VAL ASP PRO GLU LEU SEQRES 13 A 375 ALA ALA SER GLY ALA THR LEU PRO LYS PHE ASP LYS ASP SEQRES 14 A 375 HIS ASP VAL MET LEU PHE LEU LYS MET TYR ASP PRO LYS SEQRES 15 A 375 THR ARG SER LEU ASN TYR CYS GLY HIS ILE TYR THR PRO SEQRES 16 A 375 ILE SER CYS LYS ILE ARG ASP LEU LEU PRO VAL MET CYS SEQRES 17 A 375 ASP ARG ALA GLY PHE ILE GLN ASP THR SER LEU ILE LEU SEQRES 18 A 375 TYR GLU GLU VAL LYS PRO ASN LEU THR GLU ARG ILE GLN SEQRES 19 A 375 ASP TYR ASP VAL SER LEU ASP LYS ALA LEU ASP GLU LEU SEQRES 20 A 375 MET ASP GLY ASP ILE ILE VAL PHE GLN LYS ASP ASP PRO SEQRES 21 A 375 GLU ASN ASP ASN SER GLU LEU PRO THR ALA LYS GLU TYR SEQRES 22 A 375 PHE ARG ASP LEU TYR HIS ARG VAL ASP VAL ILE PHE CYS SEQRES 23 A 375 ASP LYS THR ILE PRO ASN ASP PRO GLY PHE VAL VAL THR SEQRES 24 A 375 LEU SER ASN ARG MET ASN TYR PHE GLN VAL ALA LYS THR SEQRES 25 A 375 VAL ALA GLN ARG LEU ASN THR ASP PRO MET LEU LEU GLN SEQRES 26 A 375 PHE PHE LYS SER GLN GLY TYR ARG ASP GLY PRO GLY ASN SEQRES 27 A 375 PRO LEU ARG HIS ASN TYR GLU GLY THR LEU ARG ASP LEU SEQRES 28 A 375 LEU GLN PHE PHE LYS PRO ARG GLN PRO LYS LYS LEU TYR SEQRES 29 A 375 TYR GLN GLN LEU LYS MET LYS ILE THR ASP PHE SEQRES 1 B 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 375 ARG GLU ASN LEU TYR PHE GLN GLY ASP ILE PRO GLN GLN SEQRES 3 B 375 LEU VAL GLU ARG LEU GLN GLU GLU LYS ARG ILE GLU ALA SEQRES 4 B 375 GLN LYS ARG LYS GLU ARG GLN GLU ALA HIS LEU TYR MET SEQRES 5 B 375 GLN VAL GLN ILE VAL ALA GLU ASP GLN PHE CYS GLY HIS SEQRES 6 B 375 GLN GLY ASN ASP MET TYR ASP GLU GLU LYS VAL LYS TYR SEQRES 7 B 375 THR VAL PHE LYS VAL LEU LYS ASN SER SER LEU ALA GLU SEQRES 8 B 375 PHE VAL GLN SER LEU SER GLN THR MET GLY PHE PRO GLN SEQRES 9 B 375 ASP GLN ILE ARG LEU TRP PRO MET GLN ALA ARG SER ASN SEQRES 10 B 375 GLY THR LYS ARG PRO ALA MET LEU ASP ASN GLU ALA ASP SEQRES 11 B 375 GLY ASN LYS THR MET ILE GLU LEU SER ASP ASN GLU ASN SEQRES 12 B 375 PRO TRP THR ILE PHE LEU GLU THR VAL ASP PRO GLU LEU SEQRES 13 B 375 ALA ALA SER GLY ALA THR LEU PRO LYS PHE ASP LYS ASP SEQRES 14 B 375 HIS ASP VAL MET LEU PHE LEU LYS MET TYR ASP PRO LYS SEQRES 15 B 375 THR ARG SER LEU ASN TYR CYS GLY HIS ILE TYR THR PRO SEQRES 16 B 375 ILE SER CYS LYS ILE ARG ASP LEU LEU PRO VAL MET CYS SEQRES 17 B 375 ASP ARG ALA GLY PHE ILE GLN ASP THR SER LEU ILE LEU SEQRES 18 B 375 TYR GLU GLU VAL LYS PRO ASN LEU THR GLU ARG ILE GLN SEQRES 19 B 375 ASP TYR ASP VAL SER LEU ASP LYS ALA LEU ASP GLU LEU SEQRES 20 B 375 MET ASP GLY ASP ILE ILE VAL PHE GLN LYS ASP ASP PRO SEQRES 21 B 375 GLU ASN ASP ASN SER GLU LEU PRO THR ALA LYS GLU TYR SEQRES 22 B 375 PHE ARG ASP LEU TYR HIS ARG VAL ASP VAL ILE PHE CYS SEQRES 23 B 375 ASP LYS THR ILE PRO ASN ASP PRO GLY PHE VAL VAL THR SEQRES 24 B 375 LEU SER ASN ARG MET ASN TYR PHE GLN VAL ALA LYS THR SEQRES 25 B 375 VAL ALA GLN ARG LEU ASN THR ASP PRO MET LEU LEU GLN SEQRES 26 B 375 PHE PHE LYS SER GLN GLY TYR ARG ASP GLY PRO GLY ASN SEQRES 27 B 375 PRO LEU ARG HIS ASN TYR GLU GLY THR LEU ARG ASP LEU SEQRES 28 B 375 LEU GLN PHE PHE LYS PRO ARG GLN PRO LYS LYS LEU TYR SEQRES 29 B 375 TYR GLN GLN LEU LYS MET LYS ILE THR ASP PHE SEQRES 1 C 11 GLY PRO ARG LYS CYS ALA ARG LYS THR ARG HIS SEQRES 1 D 11 GLY PRO ARG LYS CYS ALA ARG LYS THR ARG HIS HET CL A2001 1 HET CL A2002 1 HET CL A2003 1 HET CL B2001 1 HETNAM CL CHLORIDE ION FORMUL 5 CL 4(CL 1-) FORMUL 9 HOH *39(H2 O) HELIX 1 AA1 GLU A 542 ALA A 561 1 20 HELIX 2 AA2 ASP A 573 CYS A 576 5 4 HELIX 3 AA3 SER A 601 GLY A 614 1 14 HELIX 4 AA4 PRO A 616 ASP A 618 5 3 HELIX 5 AA5 THR A 647 SER A 652 1 6 HELIX 6 AA6 ASP A 666 ALA A 671 1 6 HELIX 7 AA7 LYS A 712 ASP A 715 5 4 HELIX 8 AA8 LEU A 716 ALA A 724 1 9 HELIX 9 AA9 SER A 752 LEU A 757 1 6 HELIX 10 AB1 ASP A 772 ASP A 776 5 5 HELIX 11 AB2 THR A 782 HIS A 792 1 11 HELIX 12 AB3 ASN A 818 ASN A 831 1 14 HELIX 13 AB4 ASP A 833 MET A 835 5 3 HELIX 14 AB5 THR A 860 GLN A 866 1 7 HELIX 15 AB6 GLN B 545 ALA B 561 1 17 HELIX 16 AB7 ASP B 573 CYS B 576 5 4 HELIX 17 AB8 SER B 601 GLY B 614 1 14 HELIX 18 AB9 PRO B 616 ASP B 618 5 3 HELIX 19 AC1 THR B 647 SER B 652 1 6 HELIX 20 AC2 ASP B 666 SER B 672 1 7 HELIX 21 AC3 LYS B 712 ASP B 715 5 4 HELIX 22 AC4 LEU B 716 ALA B 724 1 9 HELIX 23 AC5 SER B 752 LEU B 757 1 6 HELIX 24 AC6 ASP B 772 SER B 778 5 7 HELIX 25 AC7 THR B 782 HIS B 792 1 11 HELIX 26 AC8 ASN B 818 ASN B 831 1 14 HELIX 27 AC9 ASP B 833 MET B 835 5 3 HELIX 28 AD1 THR B 860 GLN B 866 1 7 SHEET 1 AA1 5 THR A 592 LEU A 597 0 SHEET 2 AA1 5 TYR A 564 ALA A 571 -1 N ILE A 569 O THR A 592 SHEET 3 AA1 5 TRP A 658 THR A 664 1 O TRP A 658 N GLN A 568 SHEET 4 AA1 5 ILE A 620 ALA A 627 -1 N MET A 625 O THR A 659 SHEET 5 AA1 5 LYS A 633 PRO A 635 -1 O ARG A 634 N GLN A 626 SHEET 1 AA2 5 SER A 698 PRO A 708 0 SHEET 2 AA2 5 ASP A 684 ASP A 693 -1 N LEU A 689 O CYS A 702 SHEET 3 AA2 5 ASP A 764 LYS A 770 1 O PHE A 768 N TYR A 692 SHEET 4 AA2 5 LEU A 732 LYS A 739 -1 N TYR A 735 O VAL A 767 SHEET 5 AA2 5 LEU A 742 ARG A 745 -1 O GLU A 744 N GLU A 736 SHEET 1 AA3 5 PHE A 809 SER A 814 0 SHEET 2 AA3 5 ARG A 793 ASP A 800 -1 N VAL A 796 O VAL A 811 SHEET 3 AA3 5 LYS A 875 GLN A 880 1 O LEU A 876 N ILE A 797 SHEET 4 AA3 5 LEU A 837 SER A 842 -1 N GLN A 838 O GLN A 879 SHEET 5 AA3 5 PRO A 849 PRO A 852 -1 O ASN A 851 N LYS A 841 SHEET 1 AA4 5 THR B 592 LEU B 597 0 SHEET 2 AA4 5 TYR B 564 ALA B 571 -1 N ILE B 569 O THR B 592 SHEET 3 AA4 5 TRP B 658 THR B 664 1 O TRP B 658 N GLN B 568 SHEET 4 AA4 5 ILE B 620 ALA B 627 -1 N MET B 625 O THR B 659 SHEET 5 AA4 5 LYS B 633 PRO B 635 -1 O ARG B 634 N GLN B 626 SHEET 1 AA5 5 SER B 698 PRO B 708 0 SHEET 2 AA5 5 ASP B 684 ASP B 693 -1 N MET B 691 O ASN B 700 SHEET 3 AA5 5 ASP B 764 LYS B 770 1 O PHE B 768 N TYR B 692 SHEET 4 AA5 5 LEU B 732 LYS B 739 -1 N TYR B 735 O VAL B 767 SHEET 5 AA5 5 LEU B 742 ARG B 745 -1 O GLU B 744 N GLU B 736 SHEET 1 AA6 5 PHE B 809 SER B 814 0 SHEET 2 AA6 5 ARG B 793 ASP B 800 -1 N VAL B 796 O VAL B 811 SHEET 3 AA6 5 LYS B 875 GLN B 880 1 O LEU B 876 N ILE B 797 SHEET 4 AA6 5 LEU B 837 SER B 842 -1 N GLN B 838 O GLN B 879 SHEET 5 AA6 5 PRO B 849 PRO B 852 -1 O ASN B 851 N LYS B 841 CISPEP 1 ASN A 656 PRO A 657 0 12.44 CISPEP 2 ASN B 656 PRO B 657 0 12.80 SITE 1 AC1 1 HIS A 792 SITE 1 AC2 1 GLN A 821 CRYST1 92.336 92.336 190.283 90.00 90.00 120.00 P 32 2 1 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 0.010830 0.006253 0.000000 0.00000 SCALE2 0.000000 0.012505 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005255 0.00000