HEADER HYDROLASE 08-AUG-13 4M5X TITLE CRYSTAL STRUCTURE OF THE USP7/HAUSP CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 207-560); COMPND 5 SYNONYM: USP7, HAUSP, DEUBIQUITINATING ENZYME 7, HERPESVIRUS- COMPND 6 ASSOCIATED UBIQUITIN-SPECIFIC PROTEASE, UBIQUITIN THIOESTERASE 7, COMPND 7 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 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: 562 KEYWDS UBIQUITIN-SPECIFIC CYSTEINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.D.MESECAR,K.L.MOLLAND,Q.ZHOU REVDAT 4 20-SEP-23 4M5X 1 REMARK SEQADV REVDAT 3 15-NOV-17 4M5X 1 REMARK REVDAT 2 24-SEP-14 4M5X 1 JRNL REVDAT 1 12-MAR-14 4M5X 0 JRNL AUTH K.MOLLAND,Q.ZHOU,A.D.MESECAR JRNL TITL A 2.2 ANGSTROM RESOLUTION STRUCTURE OF THE USP7 CATALYTIC JRNL TITL 2 DOMAIN IN A NEW SPACE GROUP ELABORATES UPON STRUCTURAL JRNL TITL 3 REARRANGEMENTS RESULTING FROM UBIQUITIN BINDING. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 70 283 2014 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 1744-3091 JRNL PMID 24598911 JRNL DOI 10.1107/S2053230X14002519 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 38887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1956 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.1830 - 5.2676 0.95 2629 147 0.2060 0.2446 REMARK 3 2 5.2676 - 4.1827 0.97 2604 153 0.1652 0.1735 REMARK 3 3 4.1827 - 3.6545 0.97 2625 142 0.1606 0.2075 REMARK 3 4 3.6545 - 3.3205 0.98 2670 144 0.1711 0.2036 REMARK 3 5 3.3205 - 3.0826 0.99 2657 123 0.1722 0.2338 REMARK 3 6 3.0826 - 2.9010 1.00 2675 148 0.1831 0.2079 REMARK 3 7 2.9010 - 2.7557 1.00 2690 127 0.1790 0.2349 REMARK 3 8 2.7557 - 2.6358 1.00 2684 131 0.1781 0.2628 REMARK 3 9 2.6358 - 2.5344 1.00 2683 145 0.1835 0.2441 REMARK 3 10 2.5344 - 2.4469 1.00 2685 119 0.1915 0.2723 REMARK 3 11 2.4469 - 2.3704 1.00 2677 162 0.1930 0.2741 REMARK 3 12 2.3704 - 2.3027 1.00 2653 141 0.1889 0.2526 REMARK 3 13 2.3027 - 2.2421 1.00 2662 147 0.1983 0.2324 REMARK 3 14 2.2421 - 2.1874 0.89 2337 127 0.2170 0.2632 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 5612 REMARK 3 ANGLE : 1.161 7564 REMARK 3 CHIRALITY : 0.084 807 REMARK 3 PLANARITY : 0.004 987 REMARK 3 DIHEDRAL : 15.748 2128 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 209 THROUGH 309 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6850 38.8374 -36.3506 REMARK 3 T TENSOR REMARK 3 T11: 0.3005 T22: 0.2679 REMARK 3 T33: 0.2010 T12: -0.0458 REMARK 3 T13: 0.0204 T23: -0.0805 REMARK 3 L TENSOR REMARK 3 L11: 2.5986 L22: 1.4188 REMARK 3 L33: 3.2963 L12: 0.0844 REMARK 3 L13: 0.6905 L23: -0.3145 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: 0.2273 S13: -0.3365 REMARK 3 S21: 0.1240 S22: -0.0612 S23: 0.0908 REMARK 3 S31: 0.4643 S32: -0.2395 S33: 0.0255 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 310 THROUGH 400 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.1985 43.8093 -40.8877 REMARK 3 T TENSOR REMARK 3 T11: 0.2275 T22: 0.2955 REMARK 3 T33: 0.3446 T12: -0.0119 REMARK 3 T13: -0.0260 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 1.8813 L22: 1.3727 REMARK 3 L33: 0.6476 L12: -1.3043 REMARK 3 L13: -0.5820 L23: -0.3274 REMARK 3 S TENSOR REMARK 3 S11: 0.0331 S12: 0.1758 S13: 0.1014 REMARK 3 S21: 0.1358 S22: -0.0785 S23: -0.4590 REMARK 3 S31: 0.0733 S32: 0.1017 S33: 0.0241 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 401 THROUGH 554 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6975 51.4510 -37.8975 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1962 REMARK 3 T33: 0.1280 T12: 0.0050 REMARK 3 T13: -0.0168 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 3.6669 L22: 3.2276 REMARK 3 L33: 1.8584 L12: 0.4286 REMARK 3 L13: -0.0127 L23: 0.0687 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: 0.0189 S13: 0.1154 REMARK 3 S21: 0.2393 S22: -0.0743 S23: -0.0248 REMARK 3 S31: 0.0418 S32: -0.0757 S33: -0.0074 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 208 THROUGH 309 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.7739 71.5827 2.8377 REMARK 3 T TENSOR REMARK 3 T11: 0.2390 T22: 0.1450 REMARK 3 T33: 0.1863 T12: -0.0249 REMARK 3 T13: 0.0504 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 2.3417 L22: 1.4794 REMARK 3 L33: 3.2197 L12: 0.1901 REMARK 3 L13: -0.0887 L23: 0.6806 REMARK 3 S TENSOR REMARK 3 S11: -0.0707 S12: -0.0352 S13: -0.2327 REMARK 3 S21: 0.2755 S22: 0.0281 S23: 0.1114 REMARK 3 S31: 0.3994 S32: -0.2304 S33: 0.0152 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 310 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 80.2492 79.2796 0.5646 REMARK 3 T TENSOR REMARK 3 T11: 0.2229 T22: 0.1927 REMARK 3 T33: 0.2429 T12: 0.0118 REMARK 3 T13: -0.0294 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.6060 L22: 1.8013 REMARK 3 L33: 0.4318 L12: -0.1664 REMARK 3 L13: -0.4195 L23: 0.3973 REMARK 3 S TENSOR REMARK 3 S11: -0.0613 S12: -0.1384 S13: 0.0248 REMARK 3 S21: 0.1880 S22: 0.1048 S23: -0.3987 REMARK 3 S31: 0.1094 S32: 0.2084 S33: -0.0559 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 437 THROUGH 554 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.9976 82.9084 -1.7162 REMARK 3 T TENSOR REMARK 3 T11: 0.1479 T22: 0.1511 REMARK 3 T33: 0.1477 T12: 0.0407 REMARK 3 T13: -0.0173 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 3.2463 L22: 2.6032 REMARK 3 L33: 0.9871 L12: 1.0390 REMARK 3 L13: -0.6122 L23: -0.3481 REMARK 3 S TENSOR REMARK 3 S11: -0.0330 S12: 0.0941 S13: 0.1869 REMARK 3 S21: 0.0182 S22: 0.0694 S23: 0.1479 REMARK 3 S31: -0.0416 S32: -0.1474 S33: -0.0299 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4M5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38925 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.187 REMARK 200 RESOLUTION RANGE LOW (A) : 76.354 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8.1_1168 REMARK 200 STARTING MODEL: PDB ENTRY 1NB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 22% PEG3350, 0.2 REMARK 280 M SODIUM BROMIDE, 0.15 MM CYMAL-7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.78950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 206 REMARK 465 SER A 207 REMARK 465 LYS A 208 REMARK 465 ASP A 502 REMARK 465 ASP A 503 REMARK 465 ASP A 504 REMARK 465 LEU A 505 REMARK 465 SER A 506 REMARK 465 VAL A 507 REMARK 465 ARG A 508 REMARK 465 ARG A 555 REMARK 465 LYS A 556 REMARK 465 GLU A 557 REMARK 465 ARG A 558 REMARK 465 GLN A 559 REMARK 465 GLU A 560 REMARK 465 GLY B 206 REMARK 465 SER B 207 REMARK 465 PRO B 413 REMARK 465 GLN B 414 REMARK 465 THR B 415 REMARK 465 ASP B 502 REMARK 465 ASP B 503 REMARK 465 ASP B 504 REMARK 465 LEU B 505 REMARK 465 SER B 506 REMARK 465 VAL B 507 REMARK 465 ARG B 508 REMARK 465 ARG B 555 REMARK 465 LYS B 556 REMARK 465 GLU B 557 REMARK 465 ARG B 558 REMARK 465 GLN B 559 REMARK 465 GLU B 560 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 OE1 GLU B 308 O HOH B 732 1.93 REMARK 500 NE2 HIS B 501 O HOH B 834 2.01 REMARK 500 N LYS A 358 OE1 GLU A 362 2.07 REMARK 500 OE2 GLU B 308 O HOH B 824 2.10 REMARK 500 OD1 ASN B 309 O HOH B 808 2.12 REMARK 500 OE1 GLN B 539 O HOH B 782 2.12 REMARK 500 O HOH A 768 O HOH A 788 2.17 REMARK 500 OD1 ASP B 423 O HOH B 834 2.18 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 GLU A 383 NE ARG A 549 1655 2.10 REMARK 500 NZ LYS B 208 OE1 GLU B 546 2655 2.16 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 LEU A 304 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 549 NE - CZ - NH2 ANGL. DEV. = -4.1 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 CYS A 223 -114.26 54.38 REMARK 500 TRP A 285 77.91 -100.61 REMARK 500 ASN A 377 31.11 -90.65 REMARK 500 ALA A 381 34.36 -97.41 REMARK 500 TYR A 411 171.71 70.73 REMARK 500 THR A 415 -23.93 -176.35 REMARK 500 ASP A 459 -155.37 -130.14 REMARK 500 HIS A 461 -103.02 -106.89 REMARK 500 ASP A 482 -114.51 49.39 REMARK 500 ILE A 494 -84.76 -106.86 REMARK 500 CYS B 223 -117.39 50.20 REMARK 500 ASP B 338 67.31 -101.80 REMARK 500 GLU B 435 -44.85 -28.56 REMARK 500 ASP B 459 -159.15 -120.73 REMARK 500 ASP B 482 -111.93 53.58 REMARK 500 ILE B 494 -78.96 -110.43 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 BR A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M5W RELATED DB: PDB DBREF 4M5X A 207 560 UNP Q93009 UBP7_HUMAN 207 560 DBREF 4M5X B 207 560 UNP Q93009 UBP7_HUMAN 207 560 SEQADV 4M5X GLY A 206 UNP Q93009 EXPRESSION TAG SEQADV 4M5X GLY B 206 UNP Q93009 EXPRESSION TAG SEQRES 1 A 355 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 A 355 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 A 355 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 A 355 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 A 355 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 A 355 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 A 355 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 A 355 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 A 355 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 A 355 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 A 355 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 A 355 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 A 355 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 A 355 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 A 355 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 A 355 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 A 355 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 A 355 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 A 355 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 A 355 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 A 355 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 A 355 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 A 355 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 A 355 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 A 355 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 A 355 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 A 355 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 A 355 GLU ARG GLN GLU SEQRES 1 B 355 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 B 355 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 B 355 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 B 355 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 B 355 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 B 355 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 B 355 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 B 355 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 B 355 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 B 355 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 B 355 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 B 355 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 B 355 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 B 355 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 B 355 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 B 355 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 B 355 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 B 355 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 B 355 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 B 355 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 B 355 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 B 355 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 B 355 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 B 355 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 B 355 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 B 355 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 B 355 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 B 355 GLU ARG GLN GLU HET BR A 601 1 HET BR A 602 1 HET BR B 601 1 HETNAM BR BROMIDE ION FORMUL 3 BR 3(BR 1-) FORMUL 6 HOH *247(H2 O) HELIX 1 1 TYR A 224 PHE A 234 1 11 HELIX 2 2 THR A 235 MET A 245 1 11 HELIX 3 3 SER A 255 SER A 270 1 16 HELIX 4 4 THR A 276 GLY A 284 1 9 HELIX 5 5 ASP A 295 LYS A 312 1 18 HELIX 6 6 GLY A 318 ARG A 325 1 8 HELIX 7 7 ASN A 359 VAL A 368 1 10 HELIX 8 8 ASP A 374 LYS A 378 5 5 HELIX 9 9 GLY A 382 HIS A 384 5 3 HELIX 10 10 ASP A 434 LEU A 437 5 4 HELIX 11 11 THR A 489 ILE A 494 1 6 HELIX 12 12 GLU A 495 TYR A 498 5 4 HELIX 13 13 LYS A 523 LEU A 528 1 6 HELIX 14 14 THR A 532 ILE A 536 5 5 HELIX 15 15 PRO A 537 ALA A 552 1 16 HELIX 16 16 TYR B 224 PHE B 234 1 11 HELIX 17 17 THR B 235 MET B 245 1 11 HELIX 18 18 SER B 255 SER B 270 1 16 HELIX 19 19 THR B 276 GLY B 284 1 9 HELIX 20 20 ASP B 295 LYS B 312 1 18 HELIX 21 21 GLY B 318 ARG B 325 1 8 HELIX 22 22 ASN B 359 VAL B 368 1 10 HELIX 23 23 ASP B 374 LYS B 378 5 5 HELIX 24 24 GLY B 382 HIS B 384 5 3 HELIX 25 25 ASP B 434 LEU B 437 5 4 HELIX 26 26 THR B 489 ILE B 494 1 6 HELIX 27 27 GLU B 495 TYR B 498 5 4 HELIX 28 28 LYS B 523 LEU B 528 1 6 HELIX 29 29 THR B 532 ILE B 536 5 5 HELIX 30 30 PRO B 537 GLN B 553 1 17 SHEET 1 A 4 ARG A 340 TYR A 347 0 SHEET 2 A 4 GLY A 326 CYS A 334 -1 N MET A 328 O GLU A 345 SHEET 3 A 4 ALA A 389 THR A 397 -1 O GLU A 390 N GLN A 333 SHEET 4 A 4 GLU A 371 LEU A 373 -1 N GLU A 371 O LYS A 391 SHEET 1 B 5 ILE A 350 LEU A 352 0 SHEET 2 B 5 VAL A 401 LEU A 406 1 O GLN A 405 N LEU A 352 SHEET 3 B 5 THR A 511 ARG A 520 -1 O TYR A 518 N LEU A 402 SHEET 4 B 5 ASN A 447 SER A 457 -1 N HIS A 451 O VAL A 517 SHEET 5 B 5 GLN A 430 PRO A 432 -1 N LEU A 431 O TYR A 448 SHEET 1 C 7 ILE A 350 LEU A 352 0 SHEET 2 C 7 VAL A 401 LEU A 406 1 O GLN A 405 N LEU A 352 SHEET 3 C 7 THR A 511 ARG A 520 -1 O TYR A 518 N LEU A 402 SHEET 4 C 7 ASN A 447 SER A 457 -1 N HIS A 451 O VAL A 517 SHEET 5 C 7 HIS A 464 LEU A 469 -1 O VAL A 466 N VAL A 455 SHEET 6 C 7 TRP A 477 ASP A 481 -1 O PHE A 480 N VAL A 467 SHEET 7 C 7 VAL A 484 CYS A 488 -1 O SER A 486 N LYS A 479 SHEET 1 D 2 TYR A 379 ASP A 380 0 SHEET 2 D 2 LEU A 386 GLN A 387 -1 O GLN A 387 N TYR A 379 SHEET 1 E 2 PHE A 409 MET A 410 0 SHEET 2 E 2 ILE A 419 LYS A 420 -1 O ILE A 419 N MET A 410 SHEET 1 F 4 ARG B 340 TYR B 347 0 SHEET 2 F 4 GLY B 326 CYS B 334 -1 N MET B 328 O GLU B 345 SHEET 3 F 4 ALA B 389 THR B 397 -1 O GLU B 390 N GLN B 333 SHEET 4 F 4 GLU B 371 LEU B 373 -1 N LEU B 373 O ALA B 389 SHEET 1 G 5 ILE B 350 LEU B 352 0 SHEET 2 G 5 VAL B 401 LEU B 406 1 O GLN B 405 N LEU B 352 SHEET 3 G 5 THR B 511 ARG B 520 -1 O LEU B 516 N LEU B 404 SHEET 4 G 5 ASN B 447 SER B 457 -1 N LEU B 454 O MET B 515 SHEET 5 G 5 GLN B 430 PRO B 432 -1 N LEU B 431 O TYR B 448 SHEET 1 H 7 ILE B 350 LEU B 352 0 SHEET 2 H 7 VAL B 401 LEU B 406 1 O GLN B 405 N LEU B 352 SHEET 3 H 7 THR B 511 ARG B 520 -1 O LEU B 516 N LEU B 404 SHEET 4 H 7 ASN B 447 SER B 457 -1 N LEU B 454 O MET B 515 SHEET 5 H 7 HIS B 464 LEU B 469 -1 O VAL B 466 N VAL B 455 SHEET 6 H 7 CYS B 478 ASP B 481 -1 O PHE B 480 N VAL B 467 SHEET 7 H 7 VAL B 484 ARG B 487 -1 O SER B 486 N LYS B 479 SHEET 1 I 2 TYR B 379 ASP B 380 0 SHEET 2 I 2 LEU B 386 GLN B 387 -1 O GLN B 387 N TYR B 379 SHEET 1 J 2 PHE B 409 TYR B 411 0 SHEET 2 J 2 ASN B 418 LYS B 420 -1 O ILE B 419 N MET B 410 CISPEP 1 ASP B 416 GLN B 417 0 3.33 SITE 1 AC1 2 HOH A 787 HOH A 798 SITE 1 AC2 3 GLN A 219 GLY A 275 LYS A 277 SITE 1 AC3 3 GLN B 219 GLY B 275 LYS B 277 CRYST1 74.951 67.579 76.805 90.00 96.21 90.00 P 1 21 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 0.013342 0.000000 0.001452 0.00000 SCALE2 0.000000 0.014797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013097 0.00000