HEADER PROTEIN BINDING 07-JUL-10 2XK5 TITLE CRYSTAL STRUCTURE OF K6-LINKED DIUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UBIQUITIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCDF-PYLT, PTXB; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PCDF-PYLT, PTXB KEYWDS SIGNAL TRANSDUCTION, BRCA1, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.VIRDEE,J.W.CHIN,D.KOMANDER REVDAT 2 11-MAY-11 2XK5 1 JRNL REMARK REVDAT 1 25-AUG-10 2XK5 0 JRNL AUTH S.VIRDEE,Y.YE,D.P.NGUYEN,D.KOMANDER,J.W.CHIN JRNL TITL ENGINEERED DIUBIQUITIN SYNTHESIS REVEALS K29-ISOPEPTIDE JRNL TITL 2 SPECIFICITY OF AN OTU DEUBIQUITINASE JRNL REF NAT.CHEM.BIOL. V. 6 750 2010 JRNL REFN ISSN 1552-4450 JRNL PMID 20802491 JRNL DOI 10.1038/NCHEMBIO.426 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.947 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.07 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.98 REMARK 3 NUMBER OF REFLECTIONS : 4083 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2179 REMARK 3 R VALUE (WORKING SET) : 0.2134 REMARK 3 FREE R VALUE : 0.2485 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.32 REMARK 3 FREE R VALUE TEST SET COUNT : 503 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 34.9490 - 4.7597 0.97 999 126 0.2068 0.2305 REMARK 3 2 4.7597 - 3.7794 0.98 892 153 0.1961 0.2315 REMARK 3 3 3.7794 - 3.3021 0.95 871 121 0.2314 0.2941 REMARK 3 4 3.3021 - 3.0003 0.88 818 103 0.2704 0.3258 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 : 0.315 REMARK 3 B_SOL : 59.501 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.30 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 91.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.0000 REMARK 3 B22 (A**2) : 0.0000 REMARK 3 B33 (A**2) : 0.0000 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 : 0.004 1126 REMARK 3 ANGLE : 0.771 1528 REMARK 3 CHIRALITY : 0.047 189 REMARK 3 PLANARITY : 0.003 199 REMARK 3 DIHEDRAL : 17.840 414 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 14.5370 -17.4455 -24.8100 REMARK 3 T TENSOR REMARK 3 T11: 0.6136 T22: 0.4426 REMARK 3 T33: 0.6496 T12: 0.0257 REMARK 3 T13: -0.0363 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 3.2494 L22: 3.4888 REMARK 3 L33: 6.7769 L12: 1.9882 REMARK 3 L13: 1.4135 L23: 1.2347 REMARK 3 S TENSOR REMARK 3 S11: -0.5791 S12: 0.1646 S13: 0.2315 REMARK 3 S21: -0.5780 S22: -0.0733 S23: 0.1932 REMARK 3 S31: -0.5330 S32: -0.3127 S33: 0.6044 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 5.5050 3.5843 -36.9824 REMARK 3 T TENSOR REMARK 3 T11: 0.7742 T22: 0.6740 REMARK 3 T33: 0.6046 T12: -0.1635 REMARK 3 T13: -0.0919 T23: 0.1223 REMARK 3 L TENSOR REMARK 3 L11: 2.1202 L22: 4.3218 REMARK 3 L33: 1.8280 L12: -0.5076 REMARK 3 L13: -1.8889 L23: 0.6929 REMARK 3 S TENSOR REMARK 3 S11: -0.0720 S12: 0.0296 S13: -0.4973 REMARK 3 S21: -0.4861 S22: 0.0348 S23: 0.3475 REMARK 3 S31: 0.0762 S32: -0.2322 S33: 0.0735 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE DIUBIQUITIN IS LINKED VIA K6, BUT REMARK 3 DUE TO DISORDER, THE LINKING GLY76 IS NOT DEFINED IN THE REMARK 3 ELECTRON DENSITY MAPS. RESIDUES LACKING ELECTRON DENSITY WERE REMARK 3 MODELLED AS ALA. THE C-TERMINUS IS MISSING IN 1 MOIETY. REMARK 4 REMARK 4 2XK5 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-10. REMARK 100 THE PDBE ID CODE IS EBI-44533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4247 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.00 REMARK 200 RESOLUTION RANGE LOW (A) : 52.41 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.9 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.1 REMARK 200 R MERGE FOR SHELL (I) : 0.58 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.60 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 ENTRY 2JF5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.8 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-20 % PEG 3350, 0.2 M ZINC REMARK 280 ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 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 52.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.42000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.42000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.42000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 52.42000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 52.42000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 52.42000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 52.42000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 52.42000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 52.42000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 52.42000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 52.42000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 52.42000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 52.42000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 52.42000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 52.42000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 26.21000 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 78.63000 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 26.21000 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 26.21000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 78.63000 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 26.21000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 78.63000 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 78.63000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 78.63000 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 78.63000 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 26.21000 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 78.63000 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 26.21000 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 26.21000 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 78.63000 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 26.21000 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 26.21000 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 78.63000 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 78.63000 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 78.63000 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 78.63000 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 26.21000 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 78.63000 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 26.21000 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 26.21000 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 26.21000 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: 630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.4 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 ARG A 74 REMARK 465 GLY A 75 REMARK 465 GLY A 76 REMARK 465 GLY B 76 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 LEU A 8 CG CD1 CD2 REMARK 470 THR A 9 OG1 CG2 REMARK 470 LYS A 11 CG CD CE NZ REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 73 CG CD1 CD2 REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 LEU B 73 CG CD1 CD2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 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 THR A 7 -157.17 -92.87 REMARK 500 GLN A 62 -168.32 -103.75 REMARK 500 THR B 7 -160.76 -78.81 REMARK 500 LYS B 11 -168.71 -61.26 REMARK 500 ARG B 72 79.38 -106.10 REMARK 500 ARG B 74 -145.14 -143.38 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 A1074 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 16 OE2 REMARK 620 2 ASP A 32 OD2 100.1 REMARK 620 3 ASP A 32 OD1 151.5 51.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1075 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 GLU A 18 OE2 51.8 REMARK 620 3 ASP A 21 OD2 132.0 90.9 REMARK 620 4 ASP A 21 OD1 90.1 80.6 50.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1076 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 GLU A 64 OE1 77.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1076 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 18 OE2 REMARK 620 2 ASP B 21 OD1 105.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1074 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1075 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1076 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1076 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1078 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XQQ RELATED DB: PDB REMARK 900 SIMULTANEOUS DETERMINATION OF PROTEIN STRUCTURE REMARK 900 AND DYNAMICS REMARK 900 RELATED ID: 2JF5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LYS63-LINKED DI-UBIQUITIN REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 2GBJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 9-10 8 GLYCINE REMARK 900 INSERTION MUTANT OFUBIQUITIN. REMARK 900 RELATED ID: 2GBK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 9-10 MOAD REMARK 900 INSERTION MUTANT OFUBIQUITIN REMARK 900 RELATED ID: 1ZGU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE HUMAN MMS2- REMARK 900 UBIQUITIN COMPLEX REMARK 900 RELATED ID: 2G45 RELATED DB: PDB REMARK 900 CO-CRYSTAL STRUCTURE OF ZNF UBP DOMAIN REMARK 900 FROM THEDEUBIQUITINATING ENZYME ISOPEPTIDASE T REMARK 900 (ISOT) IN COMPLEXWITH UBIQUITIN REMARK 900 RELATED ID: 2J7Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UBIQUITIN-SPECIFIC REMARK 900 PROTEASE ENCODED BY MURINE CYTOMEGALOVIRUS REMARK 900 TEGUMENT PROTEIN M48 IN COMPLEX WITH A REMARK 900 UBQUITIN-BASED SUICIDE SUBSTRATE REMARK 900 RELATED ID: 2WDT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM REMARK 900 UCHL3 IN COMPLEX WITH THE SUICIDE INHIBITOR UBVME REMARK 900 RELATED ID: 1F9J RELATED DB: PDB REMARK 900 STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN REMARK 900 RELATED ID: 2BGF RELATED DB: PDB REMARK 900 NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN REMARK 900 USING CHEMICAL SHIFT PERTURBATION DATA REMARK 900 TOGETHER WITH RDCS AND 15N-RELAXATION DATA REMARK 900 RELATED ID: 1TBE RELATED DB: PDB REMARK 900 TETRAUBIQUITIN REMARK 900 RELATED ID: 1FXT RELATED DB: PDB REMARK 900 STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN REMARK 900 THIOLESTERCOMPLEX REMARK 900 RELATED ID: 2AYO RELATED DB: PDB REMARK 900 STRUCTURE OF USP14 BOUND TO UBQUITIN ALDEHYDE REMARK 900 RELATED ID: 1XD3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UCHL3-UBVME COMPLEX REMARK 900 RELATED ID: 1GJZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A DIMERIC N-TERMINAL REMARK 900 FRAGMENT OF HUMAN UBIQUITIN REMARK 900 RELATED ID: 1UBI RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1G6J RELATED DB: PDB REMARK 900 STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN REMARK 900 AOT REVERSEMICELLES REMARK 900 RELATED ID: 1NBF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A UBP-FAMILY REMARK 900 DEUBIQUITINATING ENZYMEIN ISOLATION AND IN REMARK 900 COMPLEX WITH UBIQUITIN ALDEHYDE REMARK 900 RELATED ID: 1SIF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A MULTIPLE HYDROPHOBIC REMARK 900 CORE MUTANT OFUBIQUITIN REMARK 900 RELATED ID: 2XEW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF K11-LINKED DIUBIQUITIN REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 2W9N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LINEAR DI-UBIQUITIN REMARK 900 RELATED ID: 1OGW RELATED DB: PDB REMARK 900 SYNTHETIC UBIQUITIN WITH FLUORO-LEU AT 50 AND 67 REMARK 900 RELATED ID: 2GBN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE REMARK 900 INSERTION MUTANTOF UBIQUITIN REMARK 900 RELATED ID: 1YX5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-1/UBIQUITIN COMPLEX REMARK 900 RELATED ID: 2GBM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE REMARK 900 INSERTION MUTANTOF UBIQUITIN REMARK 900 RELATED ID: 1C3T RELATED DB: PDB REMARK 900 ROTAMER STRAIN AS A DETERMINANT OF PROTEIN REMARK 900 STRUCTURALSPECIFICITY REMARK 900 RELATED ID: 1Q5W RELATED DB: PDB REMARK 900 UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS REMARK 900 RELATED ID: 1YX6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-2/UBIQUITIN COMPLEX REMARK 900 RELATED ID: 1S1Q RELATED DB: PDB REMARK 900 TSG101(UEV) DOMAIN IN COMPLEX WITH UBIQUITIN DBREF 2XK5 A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2XK5 B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2XK5 GLN B 39 UNP P62988 ASP 39 CONFLICT SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO GLN SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A1074 1 HET ZN A1075 1 HET ZN A1076 1 HET ZN A1077 1 HET ZN B1076 1 HET ZN B1077 1 HET ZN B1078 1 HETNAM ZN ZINC ION FORMUL 3 ZN 7(ZN 2+) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 THR B 22 GLU B 34 1 13 HELIX 5 5 PRO B 37 GLN B 39 5 3 SHEET 1 AA 5 THR A 12 GLU A 16 0 SHEET 2 AA 5 GLN A 2 LYS A 6 -1 O ILE A 3 N LEU A 15 SHEET 3 AA 5 SER A 65 LEU A 71 1 O SER A 65 N PHE A 4 SHEET 4 AA 5 GLN A 41 PHE A 45 -1 O ARG A 42 N VAL A 70 SHEET 5 AA 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 BA 5 THR B 12 GLU B 16 0 SHEET 2 BA 5 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK ZN ZN A1074 OE2 GLU A 16 1555 1555 2.66 LINK ZN ZN A1074 OD2 ASP A 32 1555 11545 2.32 LINK ZN ZN A1074 OD1 ASP A 32 1555 11545 2.66 LINK ZN ZN A1075 OE1 GLU A 18 1555 1555 2.51 LINK ZN ZN A1075 OE2 GLU A 18 1555 1555 2.53 LINK ZN ZN A1075 OD2 ASP A 21 1555 11545 2.56 LINK ZN ZN A1075 OD1 ASP A 21 1555 11545 2.62 LINK ZN ZN A1076 OE1 GLU A 64 1555 13544 2.29 LINK ZN ZN A1076 NE2 HIS A 68 1555 1555 2.51 LINK ZN ZN A1077 OD2 ASP A 52 1555 1555 2.42 LINK ZN ZN B1076 OD1 ASP B 21 1555 1555 2.48 LINK ZN ZN B1076 OE2 GLU B 18 1555 1555 2.56 LINK ZN ZN B1077 OE2 GLU B 16 1555 7454 2.41 SITE 1 AC1 3 MET A 1 GLU A 16 ASP A 32 SITE 1 AC2 2 GLU A 18 ASP A 21 SITE 1 AC3 3 GLU B 18 ASP B 21 LYS B 29 SITE 1 AC4 2 GLU A 64 HIS A 68 SITE 1 AC5 3 MET B 1 GLU B 16 ASP B 32 SITE 1 AC6 2 LYS A 27 ASP A 52 SITE 1 AC7 1 ASP B 58 CRYST1 104.840 104.840 104.840 90.00 90.00 90.00 P 43 3 2 24 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 0.009538 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009538 0.00000 MASTER 514 0 7 5 10 0 7 6 0 0 0 12 END