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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
