HEADER HYDROLASE 21-JUL-16 5KYF TITLE CRYSTAL STRUCTURE OF USP7 CATALYTIC DOMAIN [L299A] MUTANT IN COMPLEX TITLE 2 WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 192-538; 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 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: POLYUBIQUITIN-B; COMPND 13 CHAIN: C; COMPND 14 FRAGMENT: UNP RESIDUES 1-76; COMPND 15 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; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS USP7 CATALYTIC DOMAIN, DEUBIQUITINASE, L299A MUTANT, UBIQUITIN, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ROUGE,A.OZEN REVDAT 3 04-OCT-23 5KYF 1 REMARK REVDAT 2 20-FEB-19 5KYF 1 JRNL REVDAT 1 09-AUG-17 5KYF 0 JRNL AUTH A.OZEN,L.ROUGE,C.BASHORE,B.R.HEARN,N.J.SKELTON,E.C.DUEBER JRNL TITL SELECTIVELY MODULATING CONFORMATIONAL STATES OF USP7 JRNL TITL 2 CATALYTIC DOMAIN FOR ACTIVATION. JRNL REF STRUCTURE V. 26 72 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29249604 JRNL DOI 10.1016/J.STR.2017.11.010 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 73947 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 35.1376 - 3.4937 0.99 5463 152 0.1507 0.1538 REMARK 3 2 3.4937 - 2.7734 0.99 5321 148 0.1613 0.1663 REMARK 3 3 2.7734 - 2.4229 0.99 5249 146 0.1765 0.1938 REMARK 3 4 2.4229 - 2.2014 0.99 5215 145 0.1756 0.1830 REMARK 3 5 2.2014 - 2.0437 0.98 5186 144 0.1747 0.2036 REMARK 3 6 2.0437 - 1.9232 0.98 5134 142 0.1774 0.1833 REMARK 3 7 1.9232 - 1.8269 0.98 5146 144 0.1880 0.2060 REMARK 3 8 1.8269 - 1.7473 0.97 5083 141 0.1932 0.1983 REMARK 3 9 1.7473 - 1.6801 0.97 5086 141 0.1920 0.2230 REMARK 3 10 1.6801 - 1.6221 0.97 5070 141 0.1978 0.1946 REMARK 3 11 1.6221 - 1.5714 0.97 5019 139 0.1998 0.2106 REMARK 3 12 1.5714 - 1.5265 0.96 5011 140 0.2104 0.2085 REMARK 3 13 1.5265 - 1.4863 0.96 4999 139 0.2309 0.2428 REMARK 3 14 1.4863 - 1.4500 0.96 4965 138 0.2642 0.2432 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.99 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 : 0.010 3493 REMARK 3 ANGLE : 1.057 4717 REMARK 3 CHIRALITY : 0.091 514 REMARK 3 PLANARITY : 0.008 615 REMARK 3 DIHEDRAL : 19.300 1351 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5KYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.1.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74019 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 35.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.82300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.10.1 REMARK 200 STARTING MODEL: 1NBF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 25% PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 31.24500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.24500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.28000 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 GLY B 204 REMARK 465 SER B 205 REMARK 465 HIS B 206 REMARK 465 MET B 207 REMARK 465 ASP B 503 REMARK 465 ASP B 504 REMARK 465 LEU B 505 REMARK 465 SER B 506 REMARK 465 ALA B 552 REMARK 465 GLN B 553 REMARK 465 LYS B 554 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 O SER B 290 O HOH B 701 1.73 REMARK 500 O HOH B 701 O HOH B 889 1.77 REMARK 500 O HOH B 704 O HOH B 731 1.89 REMARK 500 OE2 GLU B 390 O HOH B 702 1.93 REMARK 500 O HOH B 869 O HOH B 977 1.96 REMARK 500 O HOH B 863 O HOH B 1049 1.97 REMARK 500 O HOH B 759 O HOH B 987 1.99 REMARK 500 O HOH B 984 O HOH B 1057 2.02 REMARK 500 O HOH B 843 O HOH B 959 2.04 REMARK 500 O HOH C 135 O HOH C 163 2.06 REMARK 500 NH1 ARG C 54 O HOH C 101 2.06 REMARK 500 O HOH C 109 O HOH C 160 2.08 REMARK 500 NZ LYS C 48 O HOH C 101 2.12 REMARK 500 O HOH B 853 O HOH B 920 2.13 REMARK 500 O HOH B 710 O HOH B 1026 2.14 REMARK 500 OE1 GLU B 383 O HOH B 703 2.14 REMARK 500 O HOH B 1083 O HOH B 1084 2.17 REMARK 500 OE2 GLU C 16 O HOH C 102 2.17 REMARK 500 O HOH B 760 O HOH B 1019 2.18 REMARK 500 O HOH B 1029 O HOH B 1051 2.19 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 B 760 O HOH B 891 3545 1.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 343 CA ARG B 343 C 0.166 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 343 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG B 343 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 343 NE - CZ - NH2 ANGL. DEV. = -5.8 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 SER B 290 15.98 -146.46 REMARK 500 PHE B 291 153.05 80.53 REMARK 500 ALA B 381 56.15 -99.16 REMARK 500 ASP B 444 73.82 -153.27 REMARK 500 ASP B 482 -112.83 49.41 REMARK 500 ILE B 494 -84.94 -106.15 REMARK 500 GLU C 64 -0.56 77.42 REMARK 500 LEU C 71 -148.72 -105.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 343 0.08 SIDE CHAIN 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 GOL B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KYB RELATED DB: PDB REMARK 900 RELATED ID: 5KYC RELATED DB: PDB REMARK 900 RELATED ID: 5KYD RELATED DB: PDB REMARK 900 RELATED ID: 5KYE RELATED DB: PDB DBREF 5KYF B 208 554 UNP Q93009 UBP7_HUMAN 192 538 DBREF 5KYF C 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5KYF GLY B 204 UNP Q93009 EXPRESSION TAG SEQADV 5KYF SER B 205 UNP Q93009 EXPRESSION TAG SEQADV 5KYF HIS B 206 UNP Q93009 EXPRESSION TAG SEQADV 5KYF MET B 207 UNP Q93009 EXPRESSION TAG SEQADV 5KYF ALA B 299 UNP Q93009 LEU 283 ENGINEERED MUTATION SEQRES 1 B 351 GLY SER HIS MET LYS LYS HIS THR GLY TYR VAL GLY LEU SEQRES 2 B 351 LYS ASN GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU SEQRES 3 B 351 GLN THR LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL SEQRES 4 B 351 TYR MET MET PRO THR GLU GLY ASP ASP SER SER LYS SER SEQRES 5 B 351 VAL PRO LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN SEQRES 6 B 351 HIS SER ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SEQRES 7 B 351 SER PHE GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS SEQRES 8 B 351 ASP VAL GLN GLU ALA CYS ARG VAL LEU LEU ASP ASN VAL SEQRES 9 B 351 GLU ASN LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE SEQRES 10 B 351 PRO LYS LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN SEQRES 11 B 351 CYS LYS GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP SEQRES 12 B 351 TYR TYR ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN SEQRES 13 B 351 ILE PHE GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN SEQRES 14 B 351 LEU ASP GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY SEQRES 15 B 351 LEU GLN GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU SEQRES 16 B 351 PRO PRO VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR SEQRES 17 B 351 ASP PRO GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG SEQRES 18 B 351 PHE GLU PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU SEQRES 19 B 351 GLN LYS THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU SEQRES 20 B 351 HIS ALA VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY SEQRES 21 B 351 HIS TYR VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS SEQRES 22 B 351 TRP CYS LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR SEQRES 23 B 351 LYS GLU GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP SEQRES 24 B 351 ASP ASP LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET SEQRES 25 B 351 LEU VAL TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU SEQRES 26 B 351 GLN ALA VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL SEQRES 27 B 351 GLU ARG LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET GOL B 601 6 HET GOL B 602 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *468(H2 O) HELIX 1 AA1 THR B 222 PHE B 234 1 13 HELIX 2 AA2 THR B 235 MET B 245 1 11 HELIX 3 AA3 SER B 255 SER B 270 1 16 HELIX 4 AA4 THR B 276 GLY B 284 1 9 HELIX 5 AA5 ASP B 295 LYS B 312 1 18 HELIX 6 AA6 GLY B 318 ARG B 325 1 8 HELIX 7 AA7 ASN B 359 VAL B 368 1 10 HELIX 8 AA8 ASP B 374 LYS B 378 5 5 HELIX 9 AA9 GLY B 382 HIS B 384 5 3 HELIX 10 AB1 ASP B 434 LEU B 437 5 4 HELIX 11 AB2 THR B 489 ILE B 494 1 6 HELIX 12 AB3 GLU B 495 TYR B 498 5 4 HELIX 13 AB4 VAL B 507 HIS B 509 5 3 HELIX 14 AB5 LYS B 523 LEU B 528 1 6 HELIX 15 AB6 THR B 532 ILE B 536 5 5 HELIX 16 AB7 PRO B 537 GLU B 551 1 15 HELIX 17 AB8 THR C 22 GLY C 35 1 14 HELIX 18 AB9 PRO C 37 GLN C 41 5 5 HELIX 19 AC1 LEU C 56 ASN C 60 5 5 SHEET 1 AA1 4 ARG B 340 TYR B 347 0 SHEET 2 AA1 4 GLY B 326 CYS B 334 -1 N MET B 328 O GLU B 345 SHEET 3 AA1 4 ALA B 389 THR B 397 -1 O GLY B 392 N TYR B 331 SHEET 4 AA1 4 GLU B 371 LEU B 373 -1 N LEU B 373 O ALA B 389 SHEET 1 AA2 5 ILE B 350 LEU B 352 0 SHEET 2 AA2 5 VAL B 401 LEU B 406 1 O GLN B 405 N ILE B 350 SHEET 3 AA2 5 THR B 511 ARG B 520 -1 O TYR B 518 N LEU B 402 SHEET 4 AA2 5 ASN B 447 ASP B 459 -1 N HIS B 451 O VAL B 517 SHEET 5 AA2 5 GLN B 430 PRO B 432 -1 N LEU B 431 O TYR B 448 SHEET 1 AA3 7 ILE B 350 LEU B 352 0 SHEET 2 AA3 7 VAL B 401 LEU B 406 1 O GLN B 405 N ILE B 350 SHEET 3 AA3 7 THR B 511 ARG B 520 -1 O TYR B 518 N LEU B 402 SHEET 4 AA3 7 ASN B 447 ASP B 459 -1 N HIS B 451 O VAL B 517 SHEET 5 AA3 7 GLY B 462 LEU B 469 -1 O TYR B 468 N VAL B 453 SHEET 6 AA3 7 TRP B 477 ASP B 481 -1 O PHE B 480 N VAL B 467 SHEET 7 AA3 7 VAL B 484 CYS B 488 -1 O SER B 486 N LYS B 479 SHEET 1 AA4 2 TYR B 379 ASP B 380 0 SHEET 2 AA4 2 LEU B 386 GLN B 387 -1 O GLN B 387 N TYR B 379 SHEET 1 AA5 2 PHE B 409 ASP B 412 0 SHEET 2 AA5 2 GLN B 417 LYS B 420 -1 O GLN B 417 N ASP B 412 SHEET 1 AA6 5 THR C 12 GLU C 16 0 SHEET 2 AA6 5 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 AA6 5 THR C 66 VAL C 70 1 O LEU C 67 N LYS C 6 SHEET 4 AA6 5 ARG C 42 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA6 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK SG CYS B 223 C GLY C 76 1555 1555 1.84 SITE 1 AC1 4 VAL B 370 GLU B 495 HOH B 749 HOH B 881 SITE 1 AC2 9 TRP B 285 GLU B 298 HOH B 701 HOH B 704 SITE 2 AC2 9 HOH B 731 HOH B 740 HOH B 763 HOH B 889 SITE 3 AC2 9 ARG C 72 CRYST1 62.490 76.560 88.390 90.00 90.00 90.00 P 21 21 21 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 0.016003 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011314 0.00000