HEADER SIGNALING PROTEIN 16-JUN-16 5KHY TITLE CRYSTAL STRUCTURE OF OXIME-LINKED K6 DIUBIQUITIN CAVEAT 5KHY 19W A 6 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYUBIQUITIN-B; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; SOURCE 6 EXPRESSION_SYSTEM: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2; 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: BACTERIA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 2 KEYWDS UBIQUITIN, OXIME, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.STANLEY,S.VIRDEE REVDAT 5 15-NOV-23 5KHY 1 REMARK LINK ATOM REVDAT 4 16-OCT-19 5KHY 1 REMARK REVDAT 3 21-NOV-18 5KHY 1 REMARK LINK REVDAT 2 13-SEP-17 5KHY 1 REMARK REVDAT 1 14-SEP-16 5KHY 0 JRNL AUTH M.STANLEY,S.VIRDEE JRNL TITL GENETICALLY DIRECTED PRODUCTION OF RECOMBINANT, ISOSTERIC JRNL TITL 2 AND NONHYDROLYSABLE UBIQUITIN CONJUGATES. JRNL REF CHEMBIOCHEM V. 17 1472 2016 JRNL REFN ESSN 1439-7633 JRNL PMID 27197715 JRNL DOI 10.1002/CBIC.201600138 REMARK 2 REMARK 2 RESOLUTION. 3.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 2689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.295 REMARK 3 R VALUE (WORKING SET) : 0.282 REMARK 3 FREE R VALUE : 0.331 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 25.690 REMARK 3 FREE R VALUE TEST SET COUNT : 691 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 28.8384 - 5.9724 0.99 444 148 0.2573 0.3011 REMARK 3 2 5.9724 - 4.7474 0.99 373 157 0.2746 0.3185 REMARK 3 3 4.7474 - 4.1493 1.00 388 142 0.2734 0.3346 REMARK 3 4 4.1493 - 3.7708 1.00 392 126 0.3679 0.3864 REMARK 3 5 3.7708 - 3.5010 1.00 402 118 0.3686 0.4978 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.650 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.022 1099 REMARK 3 ANGLE : 1.944 1496 REMARK 3 CHIRALITY : 0.129 187 REMARK 3 PLANARITY : 0.007 197 REMARK 3 DIHEDRAL : 18.861 669 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 73) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5308 17.2410 -27.6922 REMARK 3 T TENSOR REMARK 3 T11: 1.2169 T22: 0.8038 REMARK 3 T33: 0.9939 T12: -0.0628 REMARK 3 T13: 0.0266 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 5.3823 L22: 5.0049 REMARK 3 L33: 9.2297 L12: -0.8090 REMARK 3 L13: -1.1624 L23: 3.4954 REMARK 3 S TENSOR REMARK 3 S11: -0.1377 S12: -0.4622 S13: 1.1496 REMARK 3 S21: 1.2128 S22: 0.2480 S23: -0.9370 REMARK 3 S31: 1.7186 S32: 1.0684 S33: 0.3515 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 76) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5071 -3.4482 -15.2228 REMARK 3 T TENSOR REMARK 3 T11: 1.7669 T22: 1.3562 REMARK 3 T33: 1.2470 T12: 0.1346 REMARK 3 T13: 0.1661 T23: -0.0675 REMARK 3 L TENSOR REMARK 3 L11: 2.1981 L22: 4.7225 REMARK 3 L33: 7.1428 L12: 2.6881 REMARK 3 L13: 0.8278 L23: -2.1207 REMARK 3 S TENSOR REMARK 3 S11: 0.4959 S12: -0.4306 S13: -0.3424 REMARK 3 S21: 0.2258 S22: -0.1151 S23: 0.2131 REMARK 3 S31: -0.3476 S32: 2.0066 S33: -0.0000 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 5KHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000219827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979490 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2689 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, ZINC ACETATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 51.98750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.98750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.98750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.98750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.98750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.98750 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 51.98750 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 51.98750 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 51.98750 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 51.98750 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 51.98750 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 51.98750 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 51.98750 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 51.98750 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 51.98750 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 51.98750 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 51.98750 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 51.98750 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 25.99375 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 77.98125 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 25.99375 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 25.99375 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 25.99375 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 77.98125 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 25.99375 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 77.98125 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 25.99375 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 77.98125 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 25.99375 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 77.98125 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 77.98125 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 25.99375 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 77.98125 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 25.99375 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 25.99375 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 25.99375 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 77.98125 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 25.99375 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 25.99375 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 77.98125 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 77.98125 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 77.98125 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 25.99375 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 77.98125 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 25.99375 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 77.98125 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 25.99375 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 25.99375 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 25.99375 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -196.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ASP A 21 CG OD1 OD2 REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 ILE A 30 CG1 CG2 CD1 REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 56 CG CD1 CD2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LEU A 69 CG CD1 CD2 REMARK 470 LEU A 71 CG CD1 CD2 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 LYS B 33 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 ASP B 52 CG OD1 OD2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 73 CG CD1 CD2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE B 36 CA CB CG1 CG2 CD1 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 CD2 LEU A 43 CB LEU A 69 0.61 REMARK 500 OE1 GLU A 18 ZN ZN A 102 0.93 REMARK 500 CD ARG B 42 NE2 GLN B 49 1.22 REMARK 500 N MET A 1 ZN ZN A 103 1.54 REMARK 500 CG ARG B 42 NE2 GLN B 49 1.63 REMARK 500 O 19W A 6 O HIS A 68 1.65 REMARK 500 CE2 PHE A 45 CD1 ILE A 61 1.74 REMARK 500 N 19W A 6 O HIS A 68 1.78 REMARK 500 O 19W A 6 CG2 VAL A 70 1.87 REMARK 500 O ILE A 44 O LEU A 69 1.88 REMARK 500 CG LEU A 43 CB LEU A 69 1.89 REMARK 500 NZ 19W A 6 C ETA B 105 1.90 REMARK 500 CD2 LEU A 43 CA LEU A 69 2.00 REMARK 500 CD2 PHE A 45 CD1 ILE A 61 2.01 REMARK 500 OE2 GLU B 24 CB ASP B 52 2.05 REMARK 500 NH1 ARG B 42 CG ARG B 72 2.05 REMARK 500 CA 19W A 6 O HIS A 68 2.06 REMARK 500 O GLN A 40 N LEU A 73 2.09 REMARK 500 C 19W A 6 O HIS A 68 2.14 REMARK 500 CA GLN A 41 CB ARG A 72 2.16 REMARK 500 O 19W A 6 CB VAL A 70 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 OE2 GLU A 64 CE1 HIS A 68 14554 0.29 REMARK 500 OE2 GLU B 64 NE2 HIS B 68 13544 0.69 REMARK 500 OD2 ASP A 32 ZN ZN A 103 6555 1.01 REMARK 500 CG ASN B 60 ND2 ASN B 60 13544 1.02 REMARK 500 OE2 GLU A 64 ND1 HIS A 68 14554 1.07 REMARK 500 OD1 ASN B 60 ND2 ASN B 60 13544 1.07 REMARK 500 CD GLU A 64 CE1 HIS A 68 14554 1.10 REMARK 500 OE1 GLU A 34 NH2 ARG B 72 23454 1.14 REMARK 500 ND2 ASN B 60 ND2 ASN B 60 13544 1.35 REMARK 500 CG PRO A 19 OD1 ASN A 25 12554 1.39 REMARK 500 NE2 GLN B 31 NZ LYS B 63 5555 1.40 REMARK 500 OE1 GLU A 64 NE2 HIS A 68 14554 1.48 REMARK 500 OE2 GLU A 64 NE2 HIS A 68 14554 1.49 REMARK 500 N MET A 1 OD2 ASP A 32 12554 1.49 REMARK 500 CD GLN B 31 NZ LYS B 63 5555 1.55 REMARK 500 OE1 GLU A 64 ZN ZN A 101 14554 1.61 REMARK 500 CD GLU A 64 NE2 HIS A 68 14554 1.63 REMARK 500 CD GLN B 31 CE LYS B 63 5555 1.65 REMARK 500 OE2 GLU B 64 CD2 HIS B 68 13544 1.73 REMARK 500 CD PRO A 19 OD1 ASN A 25 12554 1.74 REMARK 500 OE1 GLN B 31 CE LYS B 63 5555 1.79 REMARK 500 N MET A 1 OD1 ASP A 32 12554 1.86 REMARK 500 N MET A 1 CG ASP A 32 12554 1.88 REMARK 500 CG ASN B 60 CG ASN B 60 13544 1.91 REMARK 500 OE2 GLU B 64 CE1 HIS B 68 13544 1.91 REMARK 500 CD GLU B 64 NE2 HIS B 68 13544 1.91 REMARK 500 OE1 GLU A 64 CE1 HIS A 68 14554 1.92 REMARK 500 CD GLU A 34 NH2 ARG B 72 23454 1.97 REMARK 500 CG GLN B 31 NZ LYS B 63 5555 2.01 REMARK 500 OE2 GLU A 64 CG HIS A 68 14554 2.06 REMARK 500 NE2 GLN B 31 CE LYS B 63 5555 2.14 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 GLU A 18 CD GLU A 18 OE1 -0.106 REMARK 500 GLU A 18 CD GLU A 18 OE2 -0.096 REMARK 500 ARG B 72 NE ARG B 72 CZ -0.100 REMARK 500 ARG B 72 CZ ARG B 72 NH1 -0.112 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 72 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 7 -152.89 -99.11 REMARK 500 VAL A 17 150.22 79.23 REMARK 500 ASP A 39 5.70 -66.14 REMARK 500 GLU A 64 -0.82 80.31 REMARK 500 LEU A 71 -171.79 74.81 REMARK 500 ARG A 72 -166.41 166.24 REMARK 500 GLU B 34 30.37 -144.46 REMARK 500 ASP B 39 6.13 -51.87 REMARK 500 ALA B 46 50.85 31.24 REMARK 500 GLN B 62 -164.29 -124.20 REMARK 500 GLU B 64 13.23 56.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ETA B 105 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 B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 1 N REMARK 620 2 ASP B 32 OD2 84.7 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 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ETA B 105 DBREF 5KHY A 1 73 UNP P0CG47 UBB_HUMAN 1 73 DBREF 5KHY B 1 75 UNP P0CG47 UBB_HUMAN 1 75 SEQRES 1 A 73 MET GLN ILE PHE VAL 19W THR LEU THR GLY LYS THR ILE SEQRES 2 A 73 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 73 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 73 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 73 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 73 THR LEU HIS LEU VAL LEU ARG LEU SEQRES 1 B 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY MODRES 5KHY 19W A 6 LYS MODIFIED RESIDUE HET 19W A 6 9 HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HET ZN A 104 1 HET ZN A 105 1 HET ZN A 106 1 HET ZN B 101 1 HET ZN B 102 1 HET ZN B 103 1 HET ZN B 104 1 HET ETA B 105 3 HETNAM 19W 5-(AMINOOXY)-L-NORVALINE HETNAM ZN ZINC ION HETNAM ETA ETHANOLAMINE FORMUL 1 19W C5 H12 N2 O3 FORMUL 3 ZN 10(ZN 2+) FORMUL 13 ETA C2 H7 N O HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 GLN A 41 5 5 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 THR B 22 GLY B 35 1 14 HELIX 5 AA5 PRO B 37 ASP B 39 5 3 HELIX 6 AA6 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 3 THR A 12 LEU A 15 0 SHEET 2 AA1 3 ILE A 3 19W A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 3 THR A 66 LEU A 67 1 O LEU A 67 N PHE A 4 SHEET 1 AA2 2 LEU A 43 PHE A 45 0 SHEET 2 AA2 2 LYS A 48 LEU A 50 -1 O LYS A 48 N PHE A 45 SHEET 1 AA3 5 THR B 12 GLU B 16 0 SHEET 2 AA3 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 AA3 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA3 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA3 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK C VAL A 5 N 19W A 6 1555 1555 1.34 LINK C 19W A 6 N THR A 7 1555 1555 1.35 LINK C GLY B 75 N ETA B 105 1555 1555 1.33 LINK OE2 GLU A 18 ZN ZN A 102 1555 1555 2.28 LINK OD2 ASP A 39 ZN ZN A 106 1555 1555 2.15 LINK OD2 ASP A 52 ZN ZN A 105 1555 1555 2.23 LINK OD2 ASP A 58 ZN ZN A 104 1555 1555 2.46 LINK NE2 HIS A 68 ZN ZN A 101 1555 1555 1.85 LINK N MET B 1 ZN ZN B 101 1555 9555 2.26 LINK OE2 GLU B 18 ZN ZN B 102 1555 1555 2.25 LINK OE1 GLU B 24 ZN ZN B 104 1555 1555 2.20 LINK OD2 ASP B 32 ZN ZN B 101 1555 1555 2.48 CISPEP 1 HIS A 68 LEU A 69 0 -9.83 CISPEP 2 LEU A 69 VAL A 70 0 -3.10 SITE 1 AC1 2 GLU A 64 HIS A 68 SITE 1 AC2 1 GLU A 18 SITE 1 AC3 2 MET A 1 ASP A 32 SITE 1 AC4 1 ASP A 58 SITE 1 AC5 1 ASP A 52 SITE 1 AC6 1 ASP A 39 SITE 1 AC7 3 MET B 1 GLU B 16 ASP B 32 SITE 1 AC8 3 GLU B 18 ASP B 21 LYS B 29 SITE 1 AC9 1 ASP B 58 SITE 1 AD1 2 GLU B 24 LYS B 27 SITE 1 AD2 3 GLN A 2 19W A 6 GLY B 75 CRYST1 103.975 103.975 103.975 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 0.009618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009618 0.00000