HEADER CELL CYCLE 18-MAR-16 5G0F
TITLE CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 ZNF-UBP DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HDAC6;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ZNF-UBP DOMAIN, UNP RESIDUES 972-1081;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO;
SOURCE 3 ORGANISM_COMMON: ZEBRAFISH;
SOURCE 4 ORGANISM_TAXID: 7955;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: POPINF
KEYWDS CELL CYCLE, UBIQUITIN, UBIQUITIN BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.MIYAKE,J.J.KEUSCH,L.WANG,M.SAITO,D.HESS,X.WANG,B.J.MELANCON,
AUTHOR 2 P.HELQUIST,H.GUT,P.MATTHIAS
REVDAT 5 10-JAN-24 5G0F 1 REMARK LINK
REVDAT 4 23-JAN-19 5G0F 1 REMARK LINK
REVDAT 3 28-SEP-16 5G0F 1 JRNL
REVDAT 2 10-AUG-16 5G0F 1 JRNL
REVDAT 1 27-JUL-16 5G0F 0
JRNL AUTH Y.MIYAKE,J.J.KEUSCH,L.WANG,M.SAITO,D.HESS,X.WANG,
JRNL AUTH 2 B.J.MELANCON,P.HELQUIST,H.GUT,P.MATTHIAS
JRNL TITL STRUCTURAL INSIGHTS INTO HDAC6 TUBULIN DEACETYLATION AND ITS
JRNL TITL 2 SELECTIVE INHIBITION
JRNL REF NAT.CHEM.BIOL. V. 12 748 2016
JRNL REFN ISSN 1552-4450
JRNL PMID 27454931
JRNL DOI 10.1038/NCHEMBIO.2140
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.5
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.13
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 3 NUMBER OF REFLECTIONS : 12942
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950
REMARK 3 FREE R VALUE TEST SET COUNT : 641
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 7
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.35
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2630
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2423
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2504
REMARK 3 BIN R VALUE (WORKING SET) : 0.2421
REMARK 3 BIN FREE R VALUE : 0.2448
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.79
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 126
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 859
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 14
REMARK 3 SOLVENT ATOMS : 161
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 25.27
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.84
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.212
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.130
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.124
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.118
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.117
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 906 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1238 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 282 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 22 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 134 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 906 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 105 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 1208 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.97
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.73
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.00
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -2.4313 -27.4241 38.5376
REMARK 3 T TENSOR
REMARK 3 T11: -0.0123 T22: -0.0174
REMARK 3 T33: -0.0456 T12: 0.0060
REMARK 3 T13: -0.0230 T23: -0.0082
REMARK 3 L TENSOR
REMARK 3 L11: 0.5769 L22: 3.1091
REMARK 3 L33: 0.8970 L12: 0.2121
REMARK 3 L13: -0.1560 L23: 0.5810
REMARK 3 S TENSOR
REMARK 3 S11: -0.0060 S12: 0.0308 S13: 0.0397
REMARK 3 S21: -0.1864 S22: -0.0188 S23: 0.1160
REMARK 3 S31: -0.0329 S32: -0.0591 S33: 0.0248
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5G0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1290066422.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12942
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : 0.13000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.88000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.230
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 3C5K
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 65.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1M LI2SO4, 5M NICL2, 0.1M TRIS PH 8.5
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3
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,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 Z,X,Y
REMARK 290 6555 Z,-X,-Y
REMARK 290 7555 -Z,-X,Y
REMARK 290 8555 -Z,X,-Y
REMARK 290 9555 Y,Z,X
REMARK 290 10555 -Y,Z,-X
REMARK 290 11555 Y,-Z,-X
REMARK 290 12555 -Y,-Z,X
REMARK 290 13555 X+1/2,Y+1/2,Z+1/2
REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290 17555 Z+1/2,X+1/2,Y+1/2
REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2
REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2
REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2
REMARK 290 21555 Y+1/2,Z+1/2,X+1/2
REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2
REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2
REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2
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 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
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 0.00000
REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000
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 0.00000
REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 50.37000
REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 50.37000
REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 50.37000
REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 50.37000
REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 50.37000
REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 50.37000
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 HOH A3017 LIES ON A SPECIAL POSITION.
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 C GLY A 2087 N GLY A 2088 1.34
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 PHE A1013 -65.28 -90.96
REMARK 500 VAL A1023 -101.49 -108.65
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A3030 DISTANCE = 6.33 ANGSTROMS
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 GLY A 2087
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 NI A2085 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A 972 O
REMARK 620 2 HIS A1069 NE2 89.9
REMARK 620 3 HOH A3146 O 176.7 92.6
REMARK 620 4 HOH A3147 O 89.3 93.9 88.4
REMARK 620 5 HOH A3158 O 93.2 175.9 84.2 83.3
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A2082 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 979 SG
REMARK 620 2 HIS A 981 ND1 110.0
REMARK 620 3 CYS A1049 SG 113.8 107.3
REMARK 620 4 CYS A1052 SG 107.1 104.0 114.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A2084 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 999 SG
REMARK 620 2 CYS A1002 SG 108.9
REMARK 620 3 CYS A1019 SG 114.8 113.9
REMARK 620 4 HIS A1026 ND1 108.1 111.7 99.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A2083 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A1011 SG
REMARK 620 2 CYS A1014 SG 112.5
REMARK 620 3 HIS A1030 NE2 110.6 104.0
REMARK 620 4 HIS A1036 ND1 109.5 108.6 111.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A2086 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A1057 NE2
REMARK 620 2 HIS A1062 NE2 106.2
REMARK 620 3 HOH A3130 O 74.6 92.3
REMARK 620 4 HOH A3131 O 79.3 164.9 75.4
REMARK 620 5 HOH A3132 O 116.4 83.1 168.9 107.4
REMARK 620 6 HOH A3138 O 146.5 103.5 89.0 68.2 82.3
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 A 2082
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2083
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2084
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2085
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2086
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: Binding site for Di-peptide GLY A2087 and GLY
REMARK 800 A2088
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5G0G RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 IN COMPLEX WITH
REMARK 900 TRICHOSTATIN A
REMARK 900 RELATED ID: 5G0H RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD2 IN COMPLEX WITH (S)-
REMARK 900 TRICHOSTATIN A
REMARK 900 RELATED ID: 5G0I RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 AND CD2 ( LINKER CLEAVED)
REMARK 900 IN COMPLEX WITH NEXTURASTAT A
REMARK 900 RELATED ID: 5G0J RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 AND CD2 ( LINKER INTACT)
REMARK 900 IN COMPLEX WITH NEXTURASTAT A
DBREF 5G0F A 974 1081 UNP F8W4B7 F8W4B7_DANRE 974 1081
SEQADV 5G0F GLY A 972 UNP F8W4B7 EXPRESSION TAG
SEQADV 5G0F PRO A 973 UNP F8W4B7 EXPRESSION TAG
SEQRES 1 A 110 GLY PRO ASP PRO LEU PRO TRP CYS PRO HIS LEU GLU SER
SEQRES 2 A 110 VAL ARG PRO VAL PRO ALA GLY GLY ILE ASP VAL PHE GLN
SEQRES 3 A 110 PRO CYS GLU GLU CYS GLY GLY GLU ALA GLU ASN TRP ILE
SEQRES 4 A 110 CYS LEU PHE CYS TYR LYS VAL LEU CYS GLY ARG TYR VAL
SEQRES 5 A 110 ASN GLN HIS MET VAL THR HIS GLY GLN GLU SER GLY HIS
SEQRES 6 A 110 PRO VAL VAL LEU SER PHE ALA ASP LEU SER VAL TRP CYS
SEQRES 7 A 110 TYR ALA CYS GLU SER TYR VAL HIS ASN LYS VAL LEU HIS
SEQRES 8 A 110 GLU ALA LYS ASN ALA ALA HIS LEU VAL LYS PHE GLY GLU
SEQRES 9 A 110 GLY ILE HIS PRO PHE ASN
HET GLY A2087 4
HET GLY A2088 5
HET ZN A2082 1
HET ZN A2083 1
HET ZN A2084 1
HET NI A2085 1
HET NI A2086 1
HETNAM GLY GLYCINE
HETNAM ZN ZINC ION
HETNAM NI NICKEL (II) ION
FORMUL 2 GLY 2(C2 H5 N O2)
FORMUL 4 ZN 3(ZN 2+)
FORMUL 7 NI 2(NI 2+)
FORMUL 9 HOH *161(H2 O)
HELIX 1 1 HIS A 981 VAL A 985 5 5
HELIX 2 2 GLN A 1025 GLY A 1035 1 11
HELIX 3 3 ASN A 1058 VAL A 1060 5 3
HELIX 4 4 LEU A 1061 GLY A 1074 1 14
SHEET 1 AA 5 VAL A1017 CYS A1019 0
SHEET 2 AA 5 ASN A1008 CYS A1011 -1 O TRP A1009 N LEU A1018
SHEET 3 AA 5 VAL A1038 SER A1041 -1 O LEU A1040 N ILE A1010
SHEET 4 AA 5 VAL A1047 CYS A1049 -1 O TRP A1048 N VAL A1039
SHEET 5 AA 5 SER A1054 TYR A1055 -1 O SER A1054 N CYS A1049
LINK O GLY A 972 NI NI A2085 3556 1555 2.04
LINK SG CYS A 979 ZN ZN A2082 1555 1555 2.36
LINK ND1 HIS A 981 ZN ZN A2082 1555 1555 2.17
LINK SG CYS A 999 ZN ZN A2084 1555 1555 2.33
LINK SG CYS A1002 ZN ZN A2084 1555 1555 2.34
LINK SG CYS A1011 ZN ZN A2083 1555 1555 2.34
LINK SG CYS A1014 ZN ZN A2083 1555 1555 2.46
LINK SG CYS A1019 ZN ZN A2084 1555 1555 2.30
LINK ND1 HIS A1026 ZN ZN A2084 1555 1555 1.95
LINK NE2 HIS A1030 ZN ZN A2083 1555 1555 2.03
LINK ND1 HIS A1036 ZN ZN A2083 1555 1555 2.11
LINK SG CYS A1049 ZN ZN A2082 1555 1555 2.24
LINK SG CYS A1052 ZN ZN A2082 1555 1555 2.46
LINK NE2 HIS A1057 NI NI A2086 1555 1555 1.94
LINK NE2 HIS A1062 NI NI A2086 1555 1555 2.11
LINK NE2 HIS A1069 NI NI A2085 1555 1555 2.13
LINK NI NI A2085 O HOH A3146 1555 1555 2.18
LINK NI NI A2085 O HOH A3147 1555 1555 2.33
LINK NI NI A2085 O HOH A3158 1555 1555 2.26
LINK NI NI A2086 O HOH A3130 1555 1555 2.68
LINK NI NI A2086 O HOH A3131 1555 1555 2.72
LINK NI NI A2086 O HOH A3132 1555 1555 2.24
LINK NI NI A2086 O HOH A3138 1555 1555 2.29
SITE 1 AC1 4 CYS A 979 HIS A 981 CYS A1049 CYS A1052
SITE 1 AC2 4 CYS A1011 CYS A1014 HIS A1030 HIS A1036
SITE 1 AC3 4 CYS A 999 CYS A1002 CYS A1019 HIS A1026
SITE 1 AC4 5 GLY A 972 HIS A1069 HOH A3146 HOH A3147
SITE 2 AC4 5 HOH A3158
SITE 1 AC5 6 HIS A1057 HIS A1062 HOH A3130 HOH A3131
SITE 2 AC5 6 HOH A3132 HOH A3138
SITE 1 AC6 7 TRP A1009 GLY A1020 ARG A1021 TRP A1048
SITE 2 AC6 7 TYR A1050 HOH A3091 HOH A3161
CRYST1 100.740 100.740 100.740 90.00 90.00 90.00 I 2 3 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 0.009927 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009927 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009927 0.00000