HEADER HYDROLASE 23-OCT-15 5EFK TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 (Y745F MUTANT) IN COMPLEX WITH ALPHA TUBULIN K40 TRIPEPTIDE TITLE 3 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2 (UNP RESIDUES 288-646); COMPND 5 SYNONYM: HISTONE DEACETYLASE 6; COMPND 6 EC: 3.5.1.98; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ALPHA TUBULIN K40 TRIPEPTIDE; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 10 ORGANISM_COMMON: ZEBRAFISH; SOURCE 11 ORGANISM_TAXID: 7955; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HAI,D.W.CHRISTIANSON REVDAT 7 15-NOV-23 5EFK 1 LINK REVDAT 6 27-SEP-23 5EFK 1 LINK REVDAT 5 25-DEC-19 5EFK 1 REMARK REVDAT 4 13-SEP-17 5EFK 1 REMARK REVDAT 3 07-SEP-16 5EFK 1 JRNL REVDAT 2 10-AUG-16 5EFK 1 JRNL REVDAT 1 27-JUL-16 5EFK 0 JRNL AUTH Y.HAI,D.W.CHRISTIANSON JRNL TITL HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS OF JRNL TITL 2 CATALYSIS AND INHIBITION. JRNL REF NAT.CHEM.BIOL. V. 12 741 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27454933 JRNL DOI 10.1038/NCHEMBIO.2134 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 37329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1868 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 45.3358 - 4.2639 1.00 2928 165 0.1563 0.1718 REMARK 3 2 4.2639 - 3.3847 1.00 2805 156 0.1366 0.1645 REMARK 3 3 3.3847 - 2.9570 1.00 2789 140 0.1533 0.1510 REMARK 3 4 2.9570 - 2.6866 1.00 2758 146 0.1548 0.1936 REMARK 3 5 2.6866 - 2.4941 1.00 2746 150 0.1532 0.1754 REMARK 3 6 2.4941 - 2.3471 1.00 2717 155 0.1511 0.1769 REMARK 3 7 2.3471 - 2.2295 1.00 2766 131 0.1472 0.1921 REMARK 3 8 2.2295 - 2.1325 1.00 2728 128 0.1504 0.2124 REMARK 3 9 2.1325 - 2.0504 1.00 2738 148 0.1648 0.2143 REMARK 3 10 2.0504 - 1.9796 1.00 2713 134 0.1563 0.1922 REMARK 3 11 1.9796 - 1.9177 1.00 2702 143 0.1661 0.1857 REMARK 3 12 1.9177 - 1.8629 0.99 2676 151 0.2090 0.2554 REMARK 3 13 1.8629 - 1.8139 0.88 2395 121 0.2673 0.2685 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.010 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 : 0.007 2895 REMARK 3 ANGLE : 1.110 3909 REMARK 3 CHIRALITY : 0.047 423 REMARK 3 PLANARITY : 0.005 509 REMARK 3 DIHEDRAL : 14.555 1044 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 443 THROUGH 466 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9368 30.7852 -17.4180 REMARK 3 T TENSOR REMARK 3 T11: 0.0850 T22: 0.0816 REMARK 3 T33: 0.0853 T12: -0.0212 REMARK 3 T13: 0.0052 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 0.0012 L22: 0.0044 REMARK 3 L33: 0.0035 L12: -0.0016 REMARK 3 L13: -0.0033 L23: 0.0015 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: 0.0233 S13: 0.0096 REMARK 3 S21: -0.0433 S22: -0.0391 S23: -0.0116 REMARK 3 S31: -0.0061 S32: -0.0021 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 467 THROUGH 495 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6765 21.0626 -20.4966 REMARK 3 T TENSOR REMARK 3 T11: 0.0675 T22: 0.0589 REMARK 3 T33: -0.0716 T12: -0.0182 REMARK 3 T13: -0.0083 T23: 0.0357 REMARK 3 L TENSOR REMARK 3 L11: 0.0040 L22: 0.0022 REMARK 3 L33: 0.0091 L12: 0.0066 REMARK 3 L13: -0.0010 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: 0.0799 S13: 0.1003 REMARK 3 S21: -0.0598 S22: 0.0134 S23: 0.0712 REMARK 3 S31: 0.0100 S32: 0.0096 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 496 THROUGH 516 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.9146 42.0464 -4.2912 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: -0.0323 REMARK 3 T33: 0.2404 T12: 0.0436 REMARK 3 T13: -0.0092 T23: -0.0502 REMARK 3 L TENSOR REMARK 3 L11: 0.0034 L22: 0.0018 REMARK 3 L33: 0.0016 L12: -0.0026 REMARK 3 L13: 0.0015 L23: -0.0022 REMARK 3 S TENSOR REMARK 3 S11: -0.0267 S12: -0.0166 S13: 0.0444 REMARK 3 S21: 0.0182 S22: 0.0065 S23: -0.0029 REMARK 3 S31: -0.0176 S32: -0.0330 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 517 THROUGH 557 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9271 37.7782 -9.9287 REMARK 3 T TENSOR REMARK 3 T11: 0.0255 T22: -0.1336 REMARK 3 T33: 0.1064 T12: -0.0883 REMARK 3 T13: -0.0056 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 0.0062 L22: 0.0036 REMARK 3 L33: 0.0008 L12: -0.0082 REMARK 3 L13: -0.0007 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: 0.0143 S12: 0.0207 S13: 0.0593 REMARK 3 S21: -0.0205 S22: 0.0015 S23: -0.0198 REMARK 3 S31: -0.0566 S32: -0.1730 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 558 THROUGH 577 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4093 24.6607 -8.2723 REMARK 3 T TENSOR REMARK 3 T11: 0.0485 T22: 0.0548 REMARK 3 T33: 0.0490 T12: -0.0016 REMARK 3 T13: -0.0042 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.0021 L22: 0.0051 REMARK 3 L33: 0.0038 L12: -0.0035 REMARK 3 L13: -0.0000 L23: 0.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: -0.0030 S13: 0.0326 REMARK 3 S21: -0.0011 S22: 0.0354 S23: -0.0136 REMARK 3 S31: -0.0142 S32: -0.0160 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 578 THROUGH 616 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4769 26.6254 -0.4864 REMARK 3 T TENSOR REMARK 3 T11: 0.0229 T22: 0.0257 REMARK 3 T33: 0.0400 T12: 0.0073 REMARK 3 T13: 0.0053 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.0032 L22: -0.0008 REMARK 3 L33: 0.0072 L12: -0.0026 REMARK 3 L13: 0.0006 L23: -0.0030 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: -0.0342 S13: 0.0384 REMARK 3 S21: 0.0044 S22: 0.0421 S23: -0.0475 REMARK 3 S31: 0.0166 S32: -0.0392 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 617 THROUGH 656 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9563 23.4888 8.1027 REMARK 3 T TENSOR REMARK 3 T11: 0.0488 T22: 0.0706 REMARK 3 T33: 0.0436 T12: -0.0044 REMARK 3 T13: -0.0060 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.0035 L22: 0.0025 REMARK 3 L33: 0.0078 L12: -0.0023 REMARK 3 L13: 0.0034 L23: -0.0014 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: -0.0396 S13: 0.0158 REMARK 3 S21: 0.0177 S22: -0.0324 S23: -0.0051 REMARK 3 S31: -0.0218 S32: -0.0020 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 657 THROUGH 684 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5054 12.8268 5.6604 REMARK 3 T TENSOR REMARK 3 T11: 0.0347 T22: 0.0616 REMARK 3 T33: -0.0103 T12: 0.0205 REMARK 3 T13: 0.0208 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: -0.0007 L22: 0.0018 REMARK 3 L33: 0.0051 L12: -0.0013 REMARK 3 L13: 0.0020 L23: -0.0035 REMARK 3 S TENSOR REMARK 3 S11: 0.0416 S12: -0.0394 S13: -0.0101 REMARK 3 S21: -0.0008 S22: -0.0002 S23: -0.0067 REMARK 3 S31: 0.0615 S32: 0.0226 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 685 THROUGH 746 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5466 13.8616 -4.3240 REMARK 3 T TENSOR REMARK 3 T11: 0.0455 T22: 0.0355 REMARK 3 T33: 0.0337 T12: -0.0097 REMARK 3 T13: -0.0044 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0076 L22: 0.0061 REMARK 3 L33: 0.0199 L12: 0.0047 REMARK 3 L13: 0.0087 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0022 S12: -0.0191 S13: 0.0251 REMARK 3 S21: -0.0141 S22: 0.0084 S23: -0.0057 REMARK 3 S31: 0.0334 S32: 0.0014 S33: 0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 747 THROUGH 776 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0569 8.3622 -11.6455 REMARK 3 T TENSOR REMARK 3 T11: 0.0696 T22: 0.0643 REMARK 3 T33: 0.0650 T12: 0.0072 REMARK 3 T13: 0.0010 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.0047 L22: 0.0032 REMARK 3 L33: 0.0055 L12: 0.0000 REMARK 3 L13: -0.0047 L23: 0.0100 REMARK 3 S TENSOR REMARK 3 S11: -0.0132 S12: -0.0133 S13: -0.0649 REMARK 3 S21: -0.0224 S22: -0.0084 S23: -0.0274 REMARK 3 S31: 0.0434 S32: 0.0647 S33: -0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 777 THROUGH 798 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1336 9.8446 14.1760 REMARK 3 T TENSOR REMARK 3 T11: 0.0522 T22: 0.0905 REMARK 3 T33: -0.0342 T12: -0.0052 REMARK 3 T13: -0.0369 T23: 0.0505 REMARK 3 L TENSOR REMARK 3 L11: 0.0012 L22: -0.0001 REMARK 3 L33: 0.0020 L12: -0.0012 REMARK 3 L13: 0.0013 L23: -0.0019 REMARK 3 S TENSOR REMARK 3 S11: 0.0204 S12: -0.0340 S13: -0.0022 REMARK 3 S21: 0.0399 S22: -0.0235 S23: 0.0009 REMARK 3 S31: 0.0258 S32: -0.0165 S33: -0.0000 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6648 31.9792 -1.6871 REMARK 3 T TENSOR REMARK 3 T11: 0.3438 T22: 0.3482 REMARK 3 T33: 0.4000 T12: -0.0187 REMARK 3 T13: -0.0148 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.4129 L22: 3.8717 REMARK 3 L33: 2.0000 L12: -0.1617 REMARK 3 L13: -0.5221 L23: -8.1493 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.0183 S13: 0.0055 REMARK 3 S21: 0.0019 S22: -0.0042 S23: 0.0069 REMARK 3 S31: -0.1944 S32: 0.0186 S33: 0.0174 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 5EFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37390 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.6550 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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 5EEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE, PH 9.0, 2% V/V 1,4 REMARK 280 -DIOXANE, 10% PEG20000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.63850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.33350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.63850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.33350 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: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 N NO3 B2006 LIES ON A SPECIAL POSITION. REMARK 375 O1 NO3 B2006 LIES ON A SPECIAL POSITION. 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 SER B 435 REMARK 465 ASN B 436 REMARK 465 ALA B 437 REMARK 465 GLY B 438 REMARK 465 GLY B 439 REMARK 465 SER B 440 REMARK 465 SER B 441 REMARK 465 PRO B 442 REMARK 465 ASP B 770 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 HIS B 771 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 2 N CB OG 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 HOH B 2235 O HOH B 2306 2.16 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 B 600 -86.44 -130.54 REMARK 500 TYR B 637 -50.43 -129.07 REMARK 500 LEU B 685 -66.45 -128.12 REMARK 500 GLU B 742 -111.90 -110.71 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 K B2002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 70.2 REMARK 620 3 ASP B 612 O 98.5 95.4 REMARK 620 4 HIS B 614 O 165.4 96.1 77.5 REMARK 620 5 SER B 633 OG 84.4 110.8 152.9 105.6 REMARK 620 6 LEU B 634 O 77.0 141.2 69.2 113.8 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 101.6 REMARK 620 3 ASP B 705 OD2 100.7 95.4 REMARK 620 4 HOH B2114 O 88.6 96.0 163.5 REMARK 620 5 ALY A 4 OH 150.0 106.7 86.4 79.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B2003 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 75.6 REMARK 620 3 VAL B 629 O 118.0 78.7 REMARK 620 4 TYR B 662 O 156.2 117.4 85.0 REMARK 620 5 HOH B2117 O 83.2 87.2 150.0 78.0 REMARK 620 6 HOH B2213 O 71.7 146.6 123.2 91.3 82.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 B 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 2007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MCM A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EDU RELATED DB: PDB REMARK 900 RELATED ID: 5EEF RELATED DB: PDB REMARK 900 RELATED ID: 5EEI RELATED DB: PDB REMARK 900 RELATED ID: 5EEK RELATED DB: PDB REMARK 900 RELATED ID: 5EEM RELATED DB: PDB REMARK 900 RELATED ID: 5EEN RELATED DB: PDB REMARK 900 RELATED ID: 5EF7 RELATED DB: PDB REMARK 900 RELATED ID: 5EF8 RELATED DB: PDB REMARK 900 RELATED ID: 5EFB RELATED DB: PDB REMARK 900 RELATED ID: 5EFG RELATED DB: PDB REMARK 900 RELATED ID: 5EFH RELATED DB: PDB REMARK 900 RELATED ID: 5EFJ RELATED DB: PDB REMARK 900 RELATED ID: 5EFN RELATED DB: PDB DBREF 5EFK B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 5EFK A 2 4 PDB 5EFK 5EFK 2 4 SEQADV 5EFK SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 5EFK ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 5EFK ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 5EFK GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 5EFK GLY B 439 UNP A7YT55 EXPRESSION TAG SEQADV 5EFK PHE B 745 UNP A7YT55 TYR 593 ENGINEERED MUTATION SEQRES 1 B 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 B 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 B 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 B 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 B 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 B 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 B 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 B 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 B 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 B 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 B 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 B 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 B 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 B 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 B 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 B 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 B 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 B 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 B 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 B 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 B 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 B 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 B 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 B 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY PHE ASN SEQRES 25 B 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 B 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 B 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 B 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG SEQRES 1 A 3 SER ASP ALY HET ALY A 4 12 HET ZN B2001 1 HET K B2002 1 HET K B2003 1 HET GOL B2004 6 HET PEG B2005 7 HET NO3 B2006 4 HET EDO B2007 4 HET MCM A 101 13 HETNAM ALY N(6)-ACETYLLYSINE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NO3 NITRATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL HETSYN MCM 7-AMINO-4-METHYLCOUMARIN FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 PEG C4 H10 O3 FORMUL 8 NO3 N O3 1- FORMUL 9 EDO C2 H6 O2 FORMUL 10 MCM C10 H9 N O2 FORMUL 11 HOH *287(H2 O) HELIX 1 AA1 ASP B 449 LEU B 454 5 6 HELIX 2 AA2 PRO B 467 LEU B 480 1 14 HELIX 3 AA3 LEU B 482 CYS B 486 5 5 HELIX 4 AA4 THR B 495 ALA B 500 1 6 HELIX 5 AA5 SER B 504 SER B 514 1 11 HELIX 6 AA6 GLU B 515 MET B 517 5 3 HELIX 7 AA7 LYS B 518 ASP B 527 1 10 HELIX 8 AA8 GLU B 537 THR B 558 1 22 HELIX 9 AA9 ASN B 587 ILE B 599 1 13 HELIX 10 AB1 GLY B 616 PHE B 623 1 8 HELIX 11 AB2 GLU B 638 ALA B 641 5 4 HELIX 12 AB3 SER B 646 ASN B 650 5 5 HELIX 13 AB4 LEU B 656 ARG B 660 5 5 HELIX 14 AB5 GLY B 674 LEU B 685 1 12 HELIX 15 AB6 LEU B 685 ALA B 694 1 10 HELIX 16 AB7 THR B 718 MET B 730 1 13 HELIX 17 AB8 SER B 731 GLY B 735 5 5 HELIX 18 AB9 ASN B 746 LEU B 762 1 17 HELIX 19 AC1 LYS B 776 ALA B 791 1 16 HELIX 20 AC2 TRP B 794 ARG B 798 5 5 SHEET 1 AA1 8 HIS B 487 ARG B 488 0 SHEET 2 AA1 8 THR B 444 VAL B 447 1 N THR B 444 O HIS B 487 SHEET 3 AA1 8 ASN B 563 ALA B 566 1 O ASN B 563 N GLY B 445 SHEET 4 AA1 8 VAL B 737 LEU B 741 1 O ILE B 739 N ALA B 566 SHEET 5 AA1 8 LEU B 697 ALA B 702 1 N VAL B 700 O LEU B 738 SHEET 6 AA1 8 VAL B 606 ASP B 610 1 N LEU B 607 O LEU B 699 SHEET 7 AA1 8 VAL B 629 ARG B 636 1 O LEU B 630 N ILE B 608 SHEET 8 AA1 8 ASN B 663 TRP B 668 1 O VAL B 664 N TYR B 631 LINK C ASP A 3 N ALY A 4 1555 1555 1.33 LINK C ALY A 4 N MCM A 101 1555 1555 1.34 LINK O ASP B 610 K K B2002 1555 1555 2.79 LINK OD1 ASP B 610 K K B2002 1555 1555 2.74 LINK OD1 ASP B 612 ZN ZN B2001 1555 1555 2.08 LINK O ASP B 612 K K B2002 1555 1555 2.58 LINK ND1 HIS B 614 ZN ZN B2001 1555 1555 2.15 LINK O HIS B 614 K K B2002 1555 1555 2.64 LINK O PHE B 623 K K B2003 1555 1555 2.69 LINK O ASP B 626 K K B2003 1555 1555 2.92 LINK O VAL B 629 K K B2003 1555 1555 2.71 LINK OG SER B 633 K K B2002 1555 1555 2.72 LINK O LEU B 634 K K B2002 1555 1555 2.73 LINK O TYR B 662 K K B2003 1555 1555 2.86 LINK OD2 ASP B 705 ZN ZN B2001 1555 1555 2.09 LINK ZN ZN B2001 O HOH B2114 1555 1555 2.16 LINK ZN ZN B2001 OH ALY A 4 1555 1555 2.17 LINK K K B2003 O HOH B2117 1555 1555 2.66 LINK K K B2003 O HOH B2213 1555 1555 2.90 CISPEP 1 ARG B 569 PRO B 570 0 -4.15 CISPEP 2 PHE B 643 PRO B 644 0 7.30 SITE 1 AC1 4 ASP B 612 HIS B 614 ASP B 705 HOH B2114 SITE 1 AC2 5 ASP B 610 ASP B 612 HIS B 614 SER B 633 SITE 2 AC2 5 LEU B 634 SITE 1 AC3 6 PHE B 623 ASP B 626 VAL B 629 TYR B 662 SITE 2 AC3 6 HOH B2117 HOH B2213 SITE 1 AC4 3 ARG B 660 TYR B 662 PHE B 793 SITE 1 AC5 7 GLN B 597 SER B 598 THR B 600 ARG B 636 SITE 2 AC5 7 GLY B 671 LYS B 672 GLY B 714 SITE 1 AC6 2 TRP B 459 PRO B 519 SITE 1 AC7 3 HIS B 727 MET B 730 SER B 731 SITE 1 AC8 8 ASP A 3 HOH A 201 HOH A 204 PRO B 464 SITE 2 AC8 8 ARG B 601 SER B 603 LEU B 712 HOH B2354 CRYST1 83.277 94.667 51.622 90.00 90.00 90.00 P 21 21 2 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 0.012008 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019372 0.00000