HEADER HYDROLASE 24-AUG-20 7JVU TITLE CRYSTAL STRUCTURE OF HUMAN HISTONE DEACETYLASE 8 (HDAC8) I45T MUTATION TITLE 2 COMPLEXED WITH SAHA 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 7JVU 1 REMARK REVDAT 2 30-DEC-20 7JVU 1 JRNL REVDAT 1 16-DEC-20 7JVU 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.337 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 130894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.037 REMARK 3 FREE R VALUE TEST SET COUNT : 6593 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 15.9950 - 4.6257 0.98 4185 226 0.1449 0.1542 REMARK 3 2 4.6257 - 3.6863 1.00 4181 235 0.1307 0.1441 REMARK 3 3 3.6863 - 3.2247 1.00 4205 192 0.1550 0.1791 REMARK 3 4 3.2247 - 2.9318 1.00 4147 232 0.1642 0.1873 REMARK 3 5 2.9318 - 2.7228 1.00 4162 229 0.1671 0.1800 REMARK 3 6 2.7228 - 2.5630 1.00 4114 248 0.1631 0.1874 REMARK 3 7 2.5630 - 2.4351 1.00 4148 246 0.1624 0.1757 REMARK 3 8 2.4351 - 2.3294 1.00 4146 221 0.1622 0.2034 REMARK 3 9 2.3294 - 2.2400 1.00 4148 225 0.1626 0.1862 REMARK 3 10 2.2400 - 2.1629 1.00 4145 218 0.1650 0.1814 REMARK 3 11 2.1629 - 2.0954 1.00 4146 230 0.1704 0.1900 REMARK 3 12 2.0954 - 2.0356 1.00 4120 236 0.1660 0.1968 REMARK 3 13 2.0356 - 1.9821 1.00 4127 209 0.1742 0.1888 REMARK 3 14 1.9821 - 1.9339 1.00 4196 206 0.1756 0.1969 REMARK 3 15 1.9339 - 1.8900 1.00 4130 200 0.1707 0.1980 REMARK 3 16 1.8900 - 1.8498 1.00 4133 221 0.1709 0.2048 REMARK 3 17 1.8498 - 1.8128 1.00 4172 222 0.1761 0.2203 REMARK 3 18 1.8128 - 1.7787 1.00 4097 195 0.1780 0.1890 REMARK 3 19 1.7787 - 1.7470 1.00 4144 224 0.1729 0.1950 REMARK 3 20 1.7470 - 1.7174 1.00 4123 238 0.1766 0.1886 REMARK 3 21 1.7174 - 1.6897 1.00 4187 204 0.1810 0.2293 REMARK 3 22 1.6897 - 1.6637 1.00 4110 211 0.1837 0.2040 REMARK 3 23 1.6637 - 1.6393 1.00 4173 204 0.1948 0.2277 REMARK 3 24 1.6393 - 1.6162 1.00 4104 217 0.1948 0.2282 REMARK 3 25 1.6162 - 1.5944 1.00 4144 231 0.2106 0.2496 REMARK 3 26 1.5944 - 1.5737 1.00 4105 235 0.2082 0.2207 REMARK 3 27 1.5737 - 1.5541 1.00 4134 220 0.2196 0.2280 REMARK 3 28 1.5541 - 1.5354 1.00 4135 209 0.2304 0.2741 REMARK 3 29 1.5354 - 1.5175 1.00 4157 205 0.2405 0.2723 REMARK 3 30 1.5175 - 1.5005 0.98 4083 204 0.2516 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) : 0.129 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.074 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.86 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 : 0.005 5914 REMARK 3 ANGLE : 0.805 8038 REMARK 3 CHIRALITY : 0.053 875 REMARK 3 PLANARITY : 0.005 1041 REMARK 3 DIHEDRAL : 7.121 4700 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 7JVU 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_1000251446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) SIDE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 131305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 55.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.79500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 49.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE, PH 7.0, 15% PEG35000, REMARK 280 4 MM 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 42.05900 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 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 LEU B 14 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 GLU A 23 CG CD OE1 OE2 REMARK 470 LEU A 31 CG CD1 CD2 REMARK 470 LYS A 36 CD CE NZ REMARK 470 LYS A 52 CE NZ REMARK 470 ARG A 55 NE CZ NH1 NH2 REMARK 470 LYS A 60 CD CE NZ REMARK 470 LYS A 81 CD CE NZ REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LYS A 221 CE NZ REMARK 470 GLN A 253 CD OE1 NE2 REMARK 470 ASP A 343 CG OD1 OD2 REMARK 470 ILE A 378 CG1 CG2 CD1 REMARK 470 LYS B 36 CE NZ REMARK 470 LYS B 58 CD CE NZ REMARK 470 LYS B 60 CD CE NZ REMARK 470 LYS B 81 CE NZ REMARK 470 ASP B 88 CG OD1 OD2 REMARK 470 ASP B 89 CG OD1 OD2 REMARK 470 GLU B 95 CD OE1 OE2 REMARK 470 LYS B 249 CE NZ REMARK 470 GLN B 253 CD OE1 NE2 REMARK 470 LYS B 258 CE NZ REMARK 470 GLN B 293 CD OE1 NE2 REMARK 470 LYS B 374 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 TYR A 100 -86.59 -102.61 REMARK 500 TYR A 224 1.36 83.99 REMARK 500 SER A 276 -77.20 -115.08 REMARK 500 ILE B 34 59.16 -140.14 REMARK 500 TYR B 100 -72.30 -65.80 REMARK 500 PHE B 152 -0.07 73.16 REMARK 500 TYR B 224 2.24 82.01 REMARK 500 SER B 276 -77.43 -116.09 REMARK 500 HIS B 334 -176.91 -170.46 REMARK 500 HIS B 334 -176.79 -170.46 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 815 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B 820 DISTANCE = 6.04 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 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 73.0 REMARK 620 3 ASP A 178 O 109.0 106.0 REMARK 620 4 HIS A 180 O 160.6 89.1 82.7 REMARK 620 5 SER A 199 OG 83.7 101.4 152.1 92.9 REMARK 620 6 LEU A 200 O 77.4 146.0 68.4 121.8 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 103.9 REMARK 620 3 ASP A 267 OD2 106.1 100.1 REMARK 620 4 SHH A 404 O1 83.7 97.5 157.0 REMARK 620 5 SHH A 404 O2 154.7 95.2 86.3 77.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 76.7 REMARK 620 3 VAL A 195 O 117.4 86.0 REMARK 620 4 TYR A 225 O 156.2 120.7 82.0 REMARK 620 5 HOH A 580 O 86.2 95.9 156.0 76.5 REMARK 620 6 HOH A 698 O 73.1 149.6 110.8 87.6 79.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 O REMARK 620 2 ASP B 176 OD1 72.6 REMARK 620 3 ASP B 178 O 108.5 106.3 REMARK 620 4 HIS B 180 O 160.7 89.5 82.8 REMARK 620 5 SER B 199 OG 84.4 101.6 151.7 92.7 REMARK 620 6 LEU B 200 O 77.5 146.2 68.8 121.6 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD2 REMARK 620 2 HIS B 180 ND1 103.2 REMARK 620 3 ASP B 267 OD2 105.7 100.7 REMARK 620 4 SHH B 404 O2 154.4 94.5 88.8 REMARK 620 5 SHH B 404 O1 81.3 98.6 157.2 77.8 REMARK 620 N 1 2 3 4 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 PHE B 189 O REMARK 620 2 THR B 192 O 78.4 REMARK 620 3 VAL B 195 O 117.4 82.1 REMARK 620 4 TYR B 225 O 155.5 121.8 81.5 REMARK 620 5 HOH B 579 O 88.9 99.0 153.1 75.0 REMARK 620 6 HOH B 681 O 72.0 150.3 113.3 86.6 78.7 REMARK 620 N 1 2 3 4 5 DBREF 7JVU A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 7JVU B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 7JVU THR A 45 UNP Q9BY41 ILE 45 ENGINEERED MUTATION SEQADV 7JVU ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU THR B 45 UNP Q9BY41 ILE 45 ENGINEERED MUTATION SEQADV 7JVU ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 7JVU 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 THR 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 GLY 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 THR 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 GLY 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 ZN A 401 1 HET K A 402 1 HET K A 403 1 HET SHH A 404 19 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET ZN B 401 1 HET K B 402 1 HET K B 403 1 HET SHH B 404 19 HET EDO B 405 4 HET EDO B 406 4 HET EDO B 407 4 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN SHH SAHA HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 SHH 2(C14 H20 N2 O3) FORMUL 7 EDO 7(C2 H6 O2) FORMUL 18 HOH *635(H2 O) HELIX 1 AA1 SER A 21 SER A 30 1 10 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 ALA A 68 1 6 HELIX 5 AA5 THR A 72 GLN A 84 1 13 HELIX 6 AA6 SER A 93 GLY A 97 5 5 HELIX 7 AA7 GLY A 107 ASP A 128 1 22 HELIX 8 AA8 ASN A 156 ARG A 166 1 11 HELIX 9 AA9 GLY A 182 PHE A 189 1 8 HELIX 10 AB1 LEU A 219 ARG A 223 5 5 HELIX 11 AB2 GLN A 236 ASN A 256 1 21 HELIX 12 AB3 GLY A 265 ILE A 269 5 5 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 TYR B 48 1 13 HELIX 19 AC1 LEU B 50 MET B 54 5 5 HELIX 20 AC2 SER B 63 ALA B 68 1 6 HELIX 21 AC3 THR B 72 GLY B 86 1 15 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 GLY B 265 ILE B 269 5 5 HELIX 28 AD1 THR B 280 GLN B 293 1 14 HELIX 29 AD2 ASN B 307 GLY B 324 1 18 HELIX 30 AD3 PHE B 336 GLY B 341 5 6 HELIX 31 AD4 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 VAL A 133 N VAL A 17 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 MET A 196 N TYR A 174 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 VAL B 133 N VAL B 17 SHEET 4 AA2 8 ALA B 297 LEU B 301 1 O ILE B 300 N ASN B 136 SHEET 5 AA2 8 ALA B 259 GLN B 263 1 N LEU B 262 O LEU B 299 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 402 1555 1555 2.80 LINK OD1 ASP A 176 K K A 402 1555 1555 2.71 LINK OD2 ASP A 178 ZN ZN A 401 1555 1555 1.98 LINK O ASP A 178 K K A 402 1555 1555 2.67 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.13 LINK O HIS A 180 K K A 402 1555 1555 2.74 LINK O PHE A 189 K K A 403 1555 1555 2.61 LINK O THR A 192 K K A 403 1555 1555 2.76 LINK O VAL A 195 K K A 403 1555 1555 2.60 LINK OG SER A 199 K K A 402 1555 1555 2.87 LINK O LEU A 200 K K A 402 1555 1555 2.65 LINK O TYR A 225 K K A 403 1555 1555 3.07 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 1.99 LINK ZN ZN A 401 O1 SHH A 404 1555 1555 2.01 LINK ZN ZN A 401 O2 SHH A 404 1555 1555 2.22 LINK K K A 403 O HOH A 580 1555 1555 2.78 LINK K K A 403 O HOH A 698 1555 1555 2.81 LINK O ASP B 176 K K B 402 1555 1555 2.80 LINK OD1 ASP B 176 K K B 402 1555 1555 2.69 LINK OD2 ASP B 178 ZN ZN B 401 1555 1555 2.03 LINK O ASP B 178 K K B 402 1555 1555 2.69 LINK ND1 HIS B 180 ZN ZN B 401 1555 1555 2.12 LINK O HIS B 180 K K B 402 1555 1555 2.78 LINK O PHE B 189 K K B 403 1555 1555 2.56 LINK O THR B 192 K K B 403 1555 1555 2.83 LINK O VAL B 195 K K B 403 1555 1555 2.59 LINK OG SER B 199 K K B 402 1555 1555 2.91 LINK O LEU B 200 K K B 402 1555 1555 2.64 LINK O TYR B 225 K K B 403 1555 1555 3.06 LINK OD2 ASP B 267 ZN ZN B 401 1555 1555 2.00 LINK ZN ZN B 401 O2 SHH B 404 1555 1555 2.17 LINK ZN ZN B 401 O1 SHH B 404 1555 1555 2.03 LINK K K B 403 O HOH B 579 1555 1555 2.70 LINK K K B 403 O HOH B 681 1555 1555 2.88 CISPEP 1 PHE A 208 PRO A 209 0 -1.05 CISPEP 2 GLY A 341 PRO A 342 0 2.30 CISPEP 3 PHE B 208 PRO B 209 0 -2.33 CISPEP 4 GLY B 341 PRO B 342 0 5.00 CRYST1 53.314 84.118 94.281 90.00 99.06 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 0.018757 0.000000 0.002992 0.00000 SCALE2 0.000000 0.011888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010741 0.00000