HEADER HYDROLASE 24-AUG-20 7JVW TITLE CRYSTAL STRUCTURE OF HUMAN HISTONE DEACETYLASE 8 (HDAC8) G320R TITLE 2 MUTATION COMPLEXED WITH M344 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HD8; COMPND 5 EC: 3.5.1.98; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDAC8, HDACL1, CDA07; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEACETYLASE, HYDROLASE, CORNELIA DE LANGE SYNDROME (CDLS) EXPDTA X-RAY DIFFRACTION AUTHOR J.D.OSKO,D.W.CHRISTIANSON,C.DECROOS,N.J.PORTER,M.LEE REVDAT 3 18-OCT-23 7JVW 1 REMARK REVDAT 2 30-DEC-20 7JVW 1 JRNL REVDAT 1 16-DEC-20 7JVW 0 JRNL AUTH J.D.OSKO,N.J.PORTER,C.DECROOS,M.S.LEE,P.R.WATSON,S.E.RAIBLE, JRNL AUTH 2 I.D.KRANTZ,M.A.DEARDORFF,D.W.CHRISTIANSON JRNL TITL STRUCTURAL ANALYSIS OF HISTONE DEACETYLASE 8 MUTANTS JRNL TITL 2 ASSOCIATED WITH CORNELIA DE LANGE SYNDROME SPECTRUM JRNL TITL 3 DISORDERS. JRNL REF J.STRUCT.BIOL. V. 213 07681 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 33316326 JRNL DOI 10.1016/J.JSB.2020.107681 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.337 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 30557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.125 REMARK 3 FREE R VALUE TEST SET COUNT : 1566 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 48.9800 - 5.3422 0.98 2743 146 0.1663 0.1942 REMARK 3 2 5.3422 - 4.2410 0.98 2667 163 0.1493 0.2021 REMARK 3 3 4.2410 - 3.7051 0.97 2661 141 0.1653 0.2194 REMARK 3 4 3.7051 - 3.3664 0.97 2648 140 0.2056 0.2749 REMARK 3 5 3.3664 - 3.1252 0.97 2634 139 0.1954 0.2524 REMARK 3 6 3.1252 - 2.9410 0.97 2630 137 0.2072 0.2892 REMARK 3 7 2.9410 - 2.7937 0.97 2624 136 0.2171 0.3371 REMARK 3 8 2.7937 - 2.6721 0.97 2607 140 0.2398 0.3200 REMARK 3 9 2.6721 - 2.5692 0.95 2623 135 0.2790 0.3343 REMARK 3 10 2.5692 - 2.4806 0.96 2609 145 0.2846 0.3697 REMARK 3 11 2.4806 - 2.4040 0.95 2545 144 0.2841 0.3634 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) : 0.382 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.67 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 : 0.008 5599 REMARK 3 ANGLE : 0.934 7610 REMARK 3 CHIRALITY : 0.053 839 REMARK 3 PLANARITY : 0.006 967 REMARK 3 DIHEDRAL : 7.598 4425 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7JVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 82.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.96100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 3EWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 5.3, 3% PEG1500, 4 MM REMARK 280 TCEP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 41.37500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLY A 99 REMARK 465 TYR A 100 REMARK 465 ASP A 101 REMARK 465 CYS A 102 REMARK 465 VAL A 377 REMARK 465 ILE A 378 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 GLY A 382 REMARK 465 SER A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 PRO B 4 REMARK 465 GLU B 5 REMARK 465 GLU B 6 REMARK 465 PRO B 7 REMARK 465 ALA B 8 REMARK 465 ASP B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 GLN B 12 REMARK 465 SER B 13 REMARK 465 GLY B 85A REMARK 465 ASP B 85B REMARK 465 HIS B 90 REMARK 465 PRO B 91 REMARK 465 ASP B 92 REMARK 465 SER B 93 REMARK 465 GLY B 99 REMARK 465 TYR B 100 REMARK 465 ASP B 101 REMARK 465 CYS B 102 REMARK 465 PRO B 103 REMARK 465 VAL B 377 REMARK 465 ILE B 378 REMARK 465 GLU B 379 REMARK 465 GLY B 380 REMARK 465 ARG B 381 REMARK 465 GLY B 382 REMARK 465 SER B 383 REMARK 465 HIS B 384 REMARK 465 HIS B 385 REMARK 465 HIS B 386 REMARK 465 HIS B 387 REMARK 465 HIS B 388 REMARK 465 HIS B 389 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 ASP A 29 CG OD1 OD2 REMARK 470 GLN A 53 OE1 NE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 HIS A 90 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 92 CG OD1 OD2 REMARK 470 ILE A 94 CG1 CG2 CD1 REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 LEU A 98 CG CD1 CD2 REMARK 470 THR A 105 OG1 CG2 REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 ILE A 108 CG1 CG2 CD1 REMARK 470 LYS A 221 CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 LYS A 258 NZ REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 ASP A 343 CG OD1 OD2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 LEU B 14 CG CD1 CD2 REMARK 470 ASP B 29 CG OD1 OD2 REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 ILE B 56 CG1 CG2 CD1 REMARK 470 LYS B 58 CD CE NZ REMARK 470 GLU B 65 CG CD OE1 OE2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 GLU B 85 CG CD OE1 OE2 REMARK 470 ASP B 87 CG OD1 OD2 REMARK 470 ASP B 88 CG OD1 OD2 REMARK 470 ILE B 94 CG1 CG2 CD1 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 LEU B 98 CG CD1 CD2 REMARK 470 THR B 105 OG1 CG2 REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 ILE B 108 CG1 CG2 CD1 REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 LYS B 258 CG CD CE NZ REMARK 470 LYS B 289 CE NZ REMARK 470 LYS B 325 CG CD CE NZ REMARK 470 GLU B 347 CG CD OE1 OE2 REMARK 470 GLU B 358 CG CD OE1 OE2 REMARK 470 GLN B 363 CD OE1 NE2 REMARK 470 GLN B 364 CG CD OE1 NE2 REMARK 470 LYS B 374 CG CD CE NZ 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 ASP A 29 -8.50 -58.42 REMARK 500 PHE A 70 -50.03 -127.57 REMARK 500 ALA A 104 90.47 -62.94 REMARK 500 GLU A 106 105.13 -58.18 REMARK 500 ASP A 128 12.55 -66.66 REMARK 500 ARG A 166 -7.73 -59.24 REMARK 500 TYR A 224 14.60 81.39 REMARK 500 LEU A 264 54.17 -118.16 REMARK 500 SER A 276 -75.52 -122.12 REMARK 500 CYS A 352 81.31 -68.40 REMARK 500 TRP B 141 71.30 -69.68 REMARK 500 SER B 204 142.76 -170.75 REMARK 500 ASN B 256 71.03 42.75 REMARK 500 LEU B 264 52.03 -115.90 REMARK 500 SER B 276 -78.44 -112.76 REMARK 500 HIS B 334 -170.76 -170.50 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 A 681 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 682 DISTANCE = 7.46 ANGSTROMS 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 A 503 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 77.6 REMARK 620 3 ASP A 178 O 113.4 110.8 REMARK 620 4 HIS A 180 O 166.4 93.5 79.2 REMARK 620 5 SER A 199 OG 87.0 103.4 143.0 85.1 REMARK 620 6 LEU A 200 O 80.3 151.8 63.1 111.1 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD1 REMARK 620 2 ASP A 178 OD2 55.7 REMARK 620 3 HIS A 180 ND1 149.0 95.7 REMARK 620 4 ASP A 267 OD2 92.1 100.1 106.1 REMARK 620 5 B3N A 501 O2 118.5 172.9 88.9 83.7 REMARK 620 6 B3N A 501 O4 82.5 95.8 89.5 156.4 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 504 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 76.9 REMARK 620 3 VAL A 195 O 115.0 88.6 REMARK 620 4 TYR A 225 O 155.3 117.5 86.5 REMARK 620 5 HOH A 620 O 88.2 89.9 155.6 72.7 REMARK 620 6 HOH A 638 O 72.4 146.6 116.0 87.8 76.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 O REMARK 620 2 ASP B 176 OD1 76.0 REMARK 620 3 ASP B 178 O 107.0 104.4 REMARK 620 4 HIS B 180 O 161.0 85.9 82.9 REMARK 620 5 SER B 199 OG 84.3 100.8 154.2 93.6 REMARK 620 6 LEU B 200 O 78.6 147.9 65.0 120.4 95.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD2 REMARK 620 2 HIS B 180 ND1 102.7 REMARK 620 3 ASP B 267 OD2 111.9 107.4 REMARK 620 4 B3N B 401 O2 148.5 101.1 79.9 REMARK 620 5 B3N B 401 O4 77.5 94.2 153.1 80.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 189 O REMARK 620 2 THR B 192 O 81.3 REMARK 620 3 VAL B 195 O 112.8 84.6 REMARK 620 4 TYR B 225 O 152.2 121.1 87.4 REMARK 620 5 HOH B 536 O 87.5 98.1 159.7 74.0 REMARK 620 6 HOH B 539 O 71.0 150.3 115.7 83.2 70.7 REMARK 620 N 1 2 3 4 5 DBREF 7JVW A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 7JVW B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 7JVW ARG A 320 UNP Q9BY41 GLY 320 ENGINEERED MUTATION SEQADV 7JVW ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW ARG B 320 UNP Q9BY41 GLY 320 ENGINEERED MUTATION SEQADV 7JVW ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVW HIS B 389 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 389 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 389 ARG CYS TRP THR TYR LEU THR ARG VAL ILE LEU GLY LYS SEQRES 26 A 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 B 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 B 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 B 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 B 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 B 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 B 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 B 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 B 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 B 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 B 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 B 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 B 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 B 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 B 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 B 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 B 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 B 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 B 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 B 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 B 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 B 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 B 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 B 389 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 B 389 ARG CYS TRP THR TYR LEU THR ARG VAL ILE LEU GLY LYS SEQRES 26 B 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 B 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 B 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 B 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 B 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS HET B3N A 501 22 HET ZN A 502 1 HET K A 503 1 HET K A 504 1 HET B3N B 401 22 HET ZN B 402 1 HET K B 403 1 HET K B 404 1 HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETSYN B3N M344 FORMUL 3 B3N 2(C16 H25 N3 O3) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 K 4(K 1+) FORMUL 11 HOH *143(H2 O) HELIX 1 AA1 SER A 21 ASP A 29 1 9 HELIX 2 AA2 LYS A 36 TYR A 48 1 13 HELIX 3 AA3 ALA A 49 MET A 54 5 6 HELIX 4 AA4 SER A 63 THR A 69 1 7 HELIX 5 AA5 THR A 72 VAL A 82 1 11 HELIX 6 AA6 SER A 83 GLN A 84 5 2 HELIX 7 AA7 HIS A 90 GLY A 97 5 8 HELIX 8 AA8 GLY A 107 ASP A 128 1 22 HELIX 9 AA9 ASN A 156 ARG A 166 1 11 HELIX 10 AB1 GLY A 182 PHE A 189 1 8 HELIX 11 AB2 LEU A 219 ARG A 223 5 5 HELIX 12 AB3 GLN A 236 ASN A 256 1 21 HELIX 13 AB4 THR A 280 GLN A 293 1 14 HELIX 14 AB5 ASN A 307 GLY A 324 1 18 HELIX 15 AB6 PHE A 336 GLY A 341 5 6 HELIX 16 AB7 GLU A 358 HIS A 375 1 18 HELIX 17 AB8 SER B 21 ASP B 29 1 9 HELIX 18 AB9 LYS B 36 ALA B 47 1 12 HELIX 19 AC1 TYR B 48 MET B 54 5 7 HELIX 20 AC2 SER B 63 ALA B 68 1 6 HELIX 21 AC3 THR B 72 GLN B 84 1 13 HELIX 22 AC4 GLY B 107 ASP B 128 1 22 HELIX 23 AC5 ASN B 156 ARG B 166 1 11 HELIX 24 AC6 GLY B 182 PHE B 189 1 8 HELIX 25 AC7 LEU B 219 ARG B 223 5 5 HELIX 26 AC8 GLN B 236 ASN B 256 1 21 HELIX 27 AC9 THR B 280 TRP B 294 1 15 HELIX 28 AD1 ASN B 307 GLY B 324 1 18 HELIX 29 AD2 PHE B 336 GLY B 341 5 6 HELIX 30 AD3 GLU B 358 HIS B 375 1 18 SHEET 1 AA1 8 ARG A 55 VAL A 57 0 SHEET 2 AA1 8 VAL A 17 ILE A 19 1 N TYR A 18 O ARG A 55 SHEET 3 AA1 8 VAL A 133 ASN A 136 1 O ILE A 135 N ILE A 19 SHEET 4 AA1 8 ALA A 297 LEU A 301 1 O ILE A 300 N ASN A 136 SHEET 5 AA1 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 299 SHEET 6 AA1 8 ILE A 172 ASP A 176 1 N VAL A 175 O GLN A 263 SHEET 7 AA1 8 VAL A 195 LYS A 202 1 O VAL A 198 N ASP A 176 SHEET 8 AA1 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 SHEET 1 AA2 8 ARG B 55 VAL B 57 0 SHEET 2 AA2 8 VAL B 17 ILE B 19 1 N TYR B 18 O ARG B 55 SHEET 3 AA2 8 VAL B 133 ASN B 136 1 O ILE B 135 N ILE B 19 SHEET 4 AA2 8 ALA B 297 LEU B 301 1 O ILE B 300 N ALA B 134 SHEET 5 AA2 8 ALA B 259 GLN B 263 1 N VAL B 260 O ALA B 297 SHEET 6 AA2 8 ILE B 172 ASP B 176 1 N VAL B 175 O GLN B 263 SHEET 7 AA2 8 VAL B 195 LYS B 202 1 O MET B 196 N TYR B 174 SHEET 8 AA2 8 SER B 226 ILE B 231 1 O VAL B 227 N THR B 197 LINK O ASP A 176 K K A 503 1555 1555 2.80 LINK OD1 ASP A 176 K K A 503 1555 1555 2.58 LINK OD1 ASP A 178 ZN ZN A 502 1555 1555 2.54 LINK OD2 ASP A 178 ZN ZN A 502 1555 1555 2.04 LINK O ASP A 178 K K A 503 1555 1555 2.87 LINK ND1 HIS A 180 ZN ZN A 502 1555 1555 2.05 LINK O HIS A 180 K K A 503 1555 1555 2.81 LINK O PHE A 189 K K A 504 1555 1555 2.56 LINK O THR A 192 K K A 504 1555 1555 2.98 LINK O VAL A 195 K K A 504 1555 1555 2.49 LINK OG SER A 199 K K A 503 1555 1555 3.09 LINK O LEU A 200 K K A 503 1555 1555 2.60 LINK O TYR A 225 K K A 504 1555 1555 3.15 LINK OD2 ASP A 267 ZN ZN A 502 1555 1555 2.10 LINK O2 B3N A 501 ZN ZN A 502 1555 1555 2.06 LINK O4 B3N A 501 ZN ZN A 502 1555 1555 2.19 LINK K K A 504 O HOH A 620 1555 1555 2.82 LINK K K A 504 O HOH A 638 1555 1555 2.98 LINK O ASP B 176 K K B 403 1555 1555 2.65 LINK OD1 ASP B 176 K K B 403 1555 1555 2.96 LINK OD2 ASP B 178 ZN ZN B 402 1555 1555 1.98 LINK O ASP B 178 K K B 403 1555 1555 2.76 LINK ND1 HIS B 180 ZN ZN B 402 1555 1555 1.96 LINK O HIS B 180 K K B 403 1555 1555 2.65 LINK O PHE B 189 K K B 404 1555 1555 2.60 LINK O THR B 192 K K B 404 1555 1555 2.75 LINK O VAL B 195 K K B 404 1555 1555 2.60 LINK OG SER B 199 K K B 403 1555 1555 2.88 LINK O LEU B 200 K K B 403 1555 1555 2.63 LINK O TYR B 225 K K B 404 1555 1555 3.06 LINK OD2 ASP B 267 ZN ZN B 402 1555 1555 2.28 LINK O2 B3N B 401 ZN ZN B 402 1555 1555 2.04 LINK O4 B3N B 401 ZN ZN B 402 1555 1555 2.24 LINK K K B 404 O HOH B 536 1555 1555 2.75 LINK K K B 404 O HOH B 539 1555 1555 2.98 CISPEP 1 PHE A 208 PRO A 209 0 -3.41 CISPEP 2 GLY A 341 PRO A 342 0 2.06 CISPEP 3 PHE B 208 PRO B 209 0 1.64 CISPEP 4 GLY B 341 PRO B 342 0 2.97 CRYST1 52.980 82.750 94.520 90.00 98.84 90.00 P 1 21 1 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 0.018875 0.000000 0.002936 0.00000 SCALE2 0.000000 0.012085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010707 0.00000