PDB Short entry for 1T67 HEADER HYDROLASE 05-MAY-04 1T67 TITLE CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH MS-344 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HDAC8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PSXB2; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBACHTA KEYWDS HISTONE DEACETYLASE, ZINC HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.SOMOZA,R.J.SKENE,B.A.KATZ,C.MOL,J.D.HO,A.J.JENNINGS,C.LUONG, AUTHOR 2 A.ARVAI,J.J.BUGGY,E.CHI,J.TANG,B.-C.SANG,E.VERNER,R.WYNANDS, AUTHOR 3 E.M.LEAHY,D.R.DOUGAN,G.SNELL,M.NAVRE,M.W.KNUTH,R.V.SWANSON, AUTHOR 4 D.E.MCREE,L.W.TARI REVDAT 5 23-AUG-23 1T67 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1T67 1 VERSN REVDAT 3 02-MAR-11 1T67 1 HETNAM HETSYN REVDAT 2 24-FEB-09 1T67 1 VERSN REVDAT 1 27-JUL-04 1T67 0 JRNL AUTH J.R.SOMOZA,R.J.SKENE,B.A.KATZ,C.MOL,J.D.HO,A.J.JENNINGS, JRNL AUTH 2 C.LUONG,A.ARVAI,J.J.BUGGY,E.CHI,J.TANG,B.-C.SANG,E.VERNER, JRNL AUTH 3 R.WYNANDS,E.M.LEAHY,D.R.DOUGAN,G.SNELL,M.NAVRE,M.W.KNUTH, JRNL AUTH 4 R.V.SWANSON,D.E.MCREE,L.W.TARI JRNL TITL STRUCTURAL SNAPSHOTS OF HUMAN HDAC8 PROVIDE INSIGHTS INTO JRNL TITL 2 THE CLASS I HISTONE DEACETYLASES JRNL REF STRUCTURE V. 12 1325 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15242608 JRNL DOI 10.1016/J.STR.2004.04.012 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 16130 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 869 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1147 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 33.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.60000 REMARK 3 B22 (A**2) : 3.60000 REMARK 3 B33 (A**2) : -5.40000 REMARK 3 B12 (A**2) : 1.80000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.397 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.276 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.225 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.762 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 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2787 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3777 ; 1.137 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 355 ; 7.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2144 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1500 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 146 ; 0.130 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.039 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.171 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.104 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1765 ; 0.337 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2809 ; 0.631 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1022 ; 1.062 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 968 ; 1.661 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 377 REMARK 3 ORIGIN FOR THE GROUP (A): 51.3420 0.9090 17.0990 REMARK 3 T TENSOR REMARK 3 T11: 0.2826 T22: 0.0437 REMARK 3 T33: 0.2062 T12: 0.0952 REMARK 3 T13: 0.0339 T23: 0.0542 REMARK 3 L TENSOR REMARK 3 L11: 1.6449 L22: 3.5614 REMARK 3 L33: 3.6797 L12: -0.9014 REMARK 3 L13: -0.6882 L23: 0.9748 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: 0.2042 S13: 0.0772 REMARK 3 S21: 0.0481 S22: -0.2060 S23: -0.2941 REMARK 3 S31: 0.2705 S32: 0.1390 S33: 0.1821 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16130 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 69.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : 0.55000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1T64 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, HEPES, PH 7.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.17433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.34867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 70.34867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.17433 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 A 415 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ASP A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 GLU A 85 REMARK 465 GLY A 86 REMARK 465 ASP A 87 REMARK 465 ASP A 88 REMARK 465 ASP A 89 REMARK 465 HIS A 90 REMARK 465 PRO A 91 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 14 CG CD1 CD2 REMARK 470 ALA A 32 CB REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 THR A 69 OG1 CG2 REMARK 470 GLN A 77 CG CD OE1 NE2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 ASP A 92 CG OD1 OD2 REMARK 470 GLU A 95 CB CG CD OE1 OE2 REMARK 470 ALA A 104 CB REMARK 470 THR A 105 CB OG1 CG2 REMARK 470 GLU A 106 CB CG CD OE1 OE2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 GLN A 253 CG CD OE1 NE2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 GLU A 358 CG CD OE1 OE2 REMARK 470 HIS A 360 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 LYS A 374 CG CD CE NZ REMARK 470 VAL A 377 CB CG1 CG2 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 LEU A 31 CD1 CD2 REMARK 480 ALA A 68 CB REMARK 480 ALA A 74 CB REMARK 480 LEU A 76 CD1 REMARK 480 ILE A 108 CG2 CD1 REMARK 480 ILE A 115 CD1 REMARK 480 ALA A 149 CB REMARK 480 ILE A 235 CD1 REMARK 480 ALA A 270 CB REMARK 480 ILE A 284 CD1 REMARK 480 VAL A 345 CG1 REMARK 480 LEU A 346 CD2 REMARK 480 ILE A 348 CG2 REMARK 480 LEU A 366 CD1 REMARK 480 ASN A 372 ND2 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 A 455 O HOH A 481 2.15 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 LEU A 31 CG LEU A 31 CD1 -0.379 REMARK 500 ALA A 74 CA ALA A 74 CB -0.216 REMARK 500 ALA A 270 CA ALA A 270 CB -0.247 REMARK 500 LEU A 346 CG LEU A 346 CD2 -0.255 REMARK 500 ASN A 372 CG ASN A 372 ND2 -0.239 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 ASP A 29 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 LEU A 31 CB - CG - CD1 ANGL. DEV. = 26.4 DEGREES REMARK 500 LEU A 31 CB - CG - CD2 ANGL. DEV. = -14.1 DEGREES REMARK 500 ALA A 74 N - CA - CB ANGL. DEV. = 27.3 DEGREES REMARK 500 ILE A 108 CG1 - CB - CG2 ANGL. DEV. = 34.3 DEGREES REMARK 500 ASP A 128 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 147 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 157 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 213 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 216 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ILE A 235 CB - CG1 - CD1 ANGL. DEV. = 30.4 DEGREES REMARK 500 ALA A 270 CB - CA - C ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 VAL A 345 CG1 - CB - CG2 ANGL. DEV. = 10.5 DEGREES REMARK 500 ILE A 348 CG1 - CB - CG2 ANGL. DEV. = -62.7 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 TYR A 20 134.20 -173.11 REMARK 500 PHE A 70 -51.40 -124.46 REMARK 500 GLU A 106 104.90 -40.02 REMARK 500 GLU A 148 105.70 -163.64 REMARK 500 PHE A 152 -3.08 74.80 REMARK 500 TYR A 224 -3.94 75.86 REMARK 500 ALA A 270 127.16 -29.71 REMARK 500 SER A 276 -73.37 -105.04 REMARK 500 ASN A 278 42.49 -140.63 REMARK 500 PRO A 350 94.94 22.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 349 PRO A 350 90.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN A 372 0.07 SIDE CHAIN 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 NA A 379 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD1 REMARK 620 2 ASP A 176 O 70.3 REMARK 620 3 ASP A 178 O 107.0 101.4 REMARK 620 4 HIS A 180 O 93.5 163.0 88.0 REMARK 620 5 SER A 199 OG 99.8 78.5 151.5 100.1 REMARK 620 6 LEU A 200 O 135.8 71.9 59.6 125.0 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 378 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 111.8 REMARK 620 3 ASP A 267 OD2 99.1 105.8 REMARK 620 4 B3N A 381 O4 81.3 89.9 162.8 REMARK 620 5 B3N A 381 N3 107.4 83.2 146.6 26.3 REMARK 620 6 B3N A 381 O2 151.7 89.3 92.6 80.1 54.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 380 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 90.0 REMARK 620 3 VAL A 195 O 110.7 92.9 REMARK 620 4 HOH A 418 O 67.9 157.1 100.4 REMARK 620 5 HOH A 480 O 97.2 99.2 149.6 78.6 REMARK 620 N 1 2 3 4 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 378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 379 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B3N A 381 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T64 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH TRICHOSTATIN A REMARK 900 RELATED ID: 1T69 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HDAC8 COMPLEXED WITH SAHA DBREF 1T67 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 1T67 LEU A 31 UNP Q9BY41 PRO 31 CONFLICT SEQRES 1 A 377 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 377 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 377 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 377 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 377 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 377 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 377 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 377 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 377 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 377 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 377 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 377 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 377 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 377 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 377 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 377 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 377 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 377 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 377 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 377 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 377 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 377 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 377 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 377 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 377 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 377 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 377 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 377 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 377 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL HET ZN A 378 1 HET NA A 379 1 HET NA A 380 1 HET B3N A 381 22 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETSYN B3N M344 FORMUL 2 ZN ZN 2+ FORMUL 3 NA 2(NA 1+) FORMUL 5 B3N C16 H25 N3 O3 FORMUL 6 HOH *137(H2 O) HELIX 1 1 SER A 21 SER A 30 1 10 HELIX 2 2 LYS A 36 TYR A 48 1 13 HELIX 3 3 ALA A 49 MET A 54 5 6 HELIX 4 4 SER A 63 ALA A 68 1 6 HELIX 5 5 THR A 72 GLN A 84 1 13 HELIX 6 6 GLY A 107 ASP A 128 1 22 HELIX 7 7 ASN A 156 ARG A 166 1 11 HELIX 8 8 GLY A 182 SER A 190 1 9 HELIX 9 9 LEU A 219 ARG A 223 5 5 HELIX 10 10 GLN A 236 ASN A 256 1 21 HELIX 11 11 THR A 280 GLN A 293 1 14 HELIX 12 12 ASN A 307 GLY A 324 1 18 HELIX 13 13 PHE A 336 GLY A 341 5 6 HELIX 14 14 GLU A 358 LYS A 374 1 17 SHEET 1 A 8 ARG A 55 VAL A 57 0 SHEET 2 A 8 VAL A 17 ILE A 19 1 N TYR A 18 O VAL A 57 SHEET 3 A 8 VAL A 133 ASN A 136 1 O VAL A 133 N VAL A 17 SHEET 4 A 8 ALA A 297 LEU A 301 1 O ILE A 300 N ASN A 136 SHEET 5 A 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 301 SHEET 6 A 8 ILE A 172 ASP A 176 1 N LEU A 173 O VAL A 261 SHEET 7 A 8 VAL A 195 LYS A 202 1 O VAL A 198 N ASP A 176 SHEET 8 A 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 LINK OD1 ASP A 176 NA NA A 379 1555 1555 2.30 LINK O ASP A 176 NA NA A 379 1555 1555 3.15 LINK OD2 ASP A 178 ZN ZN A 378 1555 1555 1.98 LINK O ASP A 178 NA NA A 379 1555 1555 2.82 LINK ND1 HIS A 180 ZN ZN A 378 1555 1555 2.06 LINK O HIS A 180 NA NA A 379 1555 1555 2.78 LINK O PHE A 189 NA NA A 380 1555 1555 2.39 LINK O THR A 192 NA NA A 380 1555 1555 2.53 LINK O VAL A 195 NA NA A 380 1555 1555 2.41 LINK OG SER A 199 NA NA A 379 1555 1555 2.96 LINK O LEU A 200 NA NA A 379 1555 1555 2.75 LINK OD2 ASP A 267 ZN ZN A 378 1555 1555 2.00 LINK ZN ZN A 378 O4 B3N A 381 1555 1555 1.99 LINK ZN ZN A 378 N3 B3N A 381 1555 1555 2.65 LINK ZN ZN A 378 O2 B3N A 381 1555 1555 2.03 LINK NA NA A 380 O HOH A 418 1555 1555 3.11 LINK NA NA A 380 O HOH A 480 1555 1555 2.51 CISPEP 1 PHE A 208 PRO A 209 0 -9.36 CISPEP 2 GLY A 341 PRO A 342 0 -2.20 CISPEP 3 VAL A 376 VAL A 377 0 -2.76 SITE 1 AC1 4 ASP A 178 HIS A 180 ASP A 267 B3N A 381 SITE 1 AC2 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC2 5 LEU A 200 SITE 1 AC3 5 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC3 5 HOH A 480 SITE 1 AC4 16 LYS A 33 TYR A 100 HIS A 142 HIS A 143 SITE 2 AC4 16 GLY A 151 PHE A 152 ASP A 178 HIS A 180 SITE 3 AC4 16 PHE A 208 ASP A 267 PRO A 273 MET A 274 SITE 4 AC4 16 GLY A 304 TYR A 306 ZN A 378 HOH A 392 CRYST1 80.644 80.644 105.523 90.00 90.00 120.00 P 31 2 1 6 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 0.012400 0.007159 0.000000 0.00000 SCALE2 0.000000 0.014318 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009477 0.00000