HEADER HYDROLASE/HYDROLASE INHIBITOR 14-JUL-17 5WGI TITLE ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF DANIO RERIO HISTONE TITLE 2 DEACETYLASE 6 CATALYTIC DOMAIN 2 IN COMPLEX WITH TSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2 (UNP RESIDUES 288-646); COMPND 5 SYNONYM: HISTONE DEACETYLASE 6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEACETYLASE, HYDROLASE INHIBITOR, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.J.PORTER,D.W.CHRISTIANSON REVDAT 4 04-OCT-23 5WGI 1 LINK REVDAT 3 03-JAN-18 5WGI 1 JRNL REVDAT 2 20-DEC-17 5WGI 1 JRNL REVDAT 1 06-DEC-17 5WGI 0 JRNL AUTH N.J.PORTER,A.MAHENDRAN,R.BRESLOW,D.W.CHRISTIANSON JRNL TITL UNUSUAL ZINC-BINDING MODE OF HDAC6-SELECTIVE HYDROXAMATE JRNL TITL 2 INHIBITORS. JRNL REF PROC. NATL. ACAD. SCI. V. 114 13459 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29203661 JRNL DOI 10.1073/PNAS.1718823114 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2776: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 138677 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.107 REMARK 3 R VALUE (WORKING SET) : 0.106 REMARK 3 FREE R VALUE : 0.126 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6928 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 47.0852 - 3.2623 0.95 4507 210 0.1253 0.1256 REMARK 3 2 3.2623 - 2.5894 0.96 4465 239 0.1055 0.1046 REMARK 3 3 2.5894 - 2.2621 0.97 4485 209 0.0934 0.1101 REMARK 3 4 2.2621 - 2.0553 0.96 4458 234 0.0822 0.1067 REMARK 3 5 2.0553 - 1.9080 0.97 4477 240 0.0826 0.0990 REMARK 3 6 1.9080 - 1.7955 0.98 4442 247 0.0794 0.1109 REMARK 3 7 1.7955 - 1.7055 0.98 4532 250 0.0771 0.0987 REMARK 3 8 1.7055 - 1.6313 0.98 4541 227 0.0765 0.1103 REMARK 3 9 1.6313 - 1.5685 0.98 4480 241 0.0760 0.1070 REMARK 3 10 1.5685 - 1.5144 0.97 4478 234 0.0756 0.1140 REMARK 3 11 1.5144 - 1.4670 0.98 4486 240 0.0761 0.1037 REMARK 3 12 1.4670 - 1.4251 0.98 4472 267 0.0790 0.1019 REMARK 3 13 1.4251 - 1.3876 0.98 4466 253 0.0870 0.1195 REMARK 3 14 1.3876 - 1.3537 0.97 4475 234 0.0861 0.1180 REMARK 3 15 1.3537 - 1.3229 0.97 4459 240 0.0889 0.1229 REMARK 3 16 1.3229 - 1.2948 0.97 4446 244 0.0994 0.1316 REMARK 3 17 1.2948 - 1.2689 0.97 4446 215 0.1123 0.1307 REMARK 3 18 1.2689 - 1.2449 0.96 4407 223 0.1085 0.1541 REMARK 3 19 1.2449 - 1.2227 0.96 4395 240 0.1157 0.1399 REMARK 3 20 1.2227 - 1.2020 0.96 4386 245 0.1268 0.1648 REMARK 3 21 1.2020 - 1.1826 0.95 4388 232 0.1365 0.1545 REMARK 3 22 1.1826 - 1.1644 0.95 4353 217 0.1436 0.1767 REMARK 3 23 1.1644 - 1.1472 0.94 4286 240 0.1465 0.1824 REMARK 3 24 1.1472 - 1.1311 0.94 4319 208 0.1642 0.1617 REMARK 3 25 1.1311 - 1.1158 0.93 4284 224 0.1673 0.1968 REMARK 3 26 1.1158 - 1.1013 0.92 4203 216 0.1812 0.1927 REMARK 3 27 1.1013 - 1.0875 0.91 4223 193 0.1928 0.1933 REMARK 3 28 1.0875 - 1.0744 0.91 4157 217 0.2098 0.2238 REMARK 3 29 1.0744 - 1.0619 0.90 4136 222 0.2238 0.2549 REMARK 3 30 1.0619 - 1.0500 0.90 4097 227 0.2453 0.2427 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3185 REMARK 3 ANGLE : 1.148 4312 REMARK 3 CHIRALITY : 0.087 450 REMARK 3 PLANARITY : 0.009 577 REMARK 3 DIHEDRAL : 23.011 1178 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 5WGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000228996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-16 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 138710 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 47.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 5EEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, BIS-TRIS, PH 6.5, REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 34.81950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 435 REMARK 465 ASP A 770 REMARK 465 HIS A 771 REMARK 465 LEU A 772 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 ASN A 436 CG OD1 ND2 REMARK 470 GLN A 450 CD OE1 NE2 REMARK 470 LYS A 658 CG CD CE NZ 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 O1 EDO A 814 O HOH A 903 1.90 REMARK 500 O1 EDO A 810 O HOH A 905 2.06 REMARK 500 O2 EDO A 813 O HOH A 906 2.12 REMARK 500 OD2 ASP A 652 O HOH A 907 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O1 EDO A 815 O HOH A 1287 2545 1.89 REMARK 500 O HOH A 1262 O HOH A 1318 2555 2.05 REMARK 500 O HIS A 503 O1 EDO A 812 1655 2.17 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 ARG A 469 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 481 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 691 NE - CZ - NH1 ANGL. DEV. = -3.9 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 SER A 531 61.00 61.53 REMARK 500 THR A 600 -96.31 -129.72 REMARK 500 THR A 600 -94.68 -129.72 REMARK 500 ALA A 641 51.32 -104.29 REMARK 500 ASN A 645 35.66 70.25 REMARK 500 LEU A 685 -62.47 -129.73 REMARK 500 ALA A 694 61.52 61.71 REMARK 500 GLU A 742 -115.62 -112.96 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 A1324 DISTANCE = 7.30 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 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 70.7 REMARK 620 3 ASP A 612 O 99.7 97.8 REMARK 620 4 HIS A 614 O 164.7 94.2 79.6 REMARK 620 5 SER A 633 OG 83.2 108.6 152.7 104.5 REMARK 620 6 LEU A 634 O 77.2 143.2 70.0 116.3 84.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 ASP A 612 OD2 54.7 REMARK 620 3 HIS A 614 ND1 98.9 153.3 REMARK 620 4 ASP A 705 OD2 104.4 87.4 97.0 REMARK 620 5 TSN A 802 O1 88.4 84.9 99.4 157.4 REMARK 620 6 TSN A 802 N1 115.9 111.2 82.1 139.4 30.5 REMARK 620 7 TSN A 802 O1 138.3 87.4 118.9 88.8 69.6 58.0 REMARK 620 8 TSN A 802 O2 167.4 119.1 87.5 85.5 79.8 53.9 32.2 REMARK 620 9 TSN A 802 N1 156.8 121.5 84.0 98.0 68.5 41.4 35.1 12.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 76.6 REMARK 620 3 VAL A 629 O 118.2 75.1 REMARK 620 4 TYR A 662 O 153.6 117.9 87.7 REMARK 620 5 HOH A1036 O 80.2 90.1 151.7 78.0 REMARK 620 6 HOH A1061 O 70.5 146.9 124.1 91.4 81.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 822 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 906 O REMARK 620 2 HOH A 966 O 80.5 REMARK 620 3 HOH A1012 O 88.1 93.2 REMARK 620 4 HOH A1041 O 178.3 99.1 90.3 REMARK 620 5 HOH A1216 O 93.4 173.9 86.8 87.0 REMARK 620 6 HOH A1298 O 94.3 89.0 177.0 87.3 91.3 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 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TSN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 813 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 814 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 815 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 816 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 817 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 818 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 819 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 820 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 821 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 822 DBREF 5WGI A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 5WGI SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 5WGI ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 5WGI ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 5WGI GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 5WGI GLY A 439 UNP A7YT55 EXPRESSION TAG SEQRES 1 A 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 A 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 A 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 A 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 A 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 A 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 A 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 A 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 A 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 A 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 A 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 A 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 A 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 A 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 A 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 A 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 A 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 A 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 A 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 A 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 A 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 A 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 A 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 A 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 A 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 A 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 A 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 A 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG HET ZN A 801 1 HET TSN A 802 88 HET K A 803 1 HET K A 804 1 HET CL A 805 1 HET CL A 806 1 HET CL A 807 1 HET EDO A 808 10 HET EDO A 809 10 HET EDO A 810 10 HET EDO A 811 10 HET EDO A 812 4 HET EDO A 813 4 HET EDO A 814 4 HET EDO A 815 4 HET EDO A 816 10 HET GOL A 817 28 HET GOL A 818 13 HET GOL A 819 14 HET PEG A 820 17 HET PEG A 821 17 HET MG A 822 1 HETNAM ZN ZINC ION HETNAM TSN TRICHOSTATIN A HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MG MAGNESIUM ION HETSYN TSN 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7- HETSYN 2 TSN OXO-2,4-HEPTADIENAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 TSN C17 H22 N2 O3 FORMUL 4 K 2(K 1+) FORMUL 6 CL 3(CL 1-) FORMUL 9 EDO 9(C2 H6 O2) FORMUL 18 GOL 3(C3 H8 O3) FORMUL 21 PEG 2(C4 H10 O3) FORMUL 23 MG MG 2+ FORMUL 24 HOH *424(H2 O) HELIX 1 AA1 ASP A 449 LEU A 454 5 6 HELIX 2 AA2 PRO A 467 LEU A 480 1 14 HELIX 3 AA3 LEU A 482 CYS A 486 5 5 HELIX 4 AA4 THR A 495 ALA A 500 1 6 HELIX 5 AA5 SER A 504 SER A 514 1 11 HELIX 6 AA6 GLU A 515 MET A 517 5 3 HELIX 7 AA7 LYS A 518 ASP A 527 1 10 HELIX 8 AA8 GLU A 537 THR A 558 1 22 HELIX 9 AA9 ASN A 587 THR A 600 1 14 HELIX 10 AB1 GLY A 616 GLU A 624 1 9 HELIX 11 AB2 GLU A 638 ALA A 641 5 4 HELIX 12 AB3 SER A 646 ASN A 650 5 5 HELIX 13 AB4 LEU A 656 ARG A 660 5 5 HELIX 14 AB5 GLY A 674 LEU A 685 1 12 HELIX 15 AB6 LEU A 685 ALA A 694 1 10 HELIX 16 AB7 THR A 718 MET A 730 1 13 HELIX 17 AB8 SER A 731 GLY A 735 5 5 HELIX 18 AB9 ASN A 746 LEU A 762 1 17 HELIX 19 AC1 LYS A 776 ALA A 791 1 16 HELIX 20 AC2 TRP A 794 ARG A 798 5 5 SHEET 1 AA1 8 HIS A 487 ARG A 488 0 SHEET 2 AA1 8 THR A 444 VAL A 447 1 N THR A 444 O HIS A 487 SHEET 3 AA1 8 ASN A 563 ALA A 566 1 O ASN A 563 N GLY A 445 SHEET 4 AA1 8 VAL A 737 LEU A 741 1 O ILE A 739 N ALA A 566 SHEET 5 AA1 8 LEU A 697 ALA A 702 1 N VAL A 700 O LEU A 738 SHEET 6 AA1 8 VAL A 606 ASP A 610 1 N LEU A 607 O LEU A 699 SHEET 7 AA1 8 VAL A 629 ARG A 636 1 O ILE A 632 N ASP A 610 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O VAL A 664 N TYR A 631 LINK O ASP A 610 K K A 803 1555 1555 2.82 LINK OD1 ASP A 610 K K A 803 1555 1555 2.69 LINK OD1 ASP A 612 ZN ZN A 801 1555 1555 2.06 LINK OD2 ASP A 612 ZN ZN A 801 1555 1555 2.60 LINK O ASP A 612 K K A 803 1555 1555 2.57 LINK ND1 HIS A 614 ZN ZN A 801 1555 1555 2.12 LINK O HIS A 614 K K A 803 1555 1555 2.68 LINK O PHE A 623 K K A 804 1555 1555 2.70 LINK O ASP A 626 K K A 804 1555 1555 2.86 LINK O VAL A 629 K K A 804 1555 1555 2.64 LINK OG SER A 633 K K A 803 1555 1555 2.73 LINK O LEU A 634 K K A 803 1555 1555 2.63 LINK O TYR A 662 K K A 804 1555 1555 2.80 LINK OD2 ASP A 705 ZN ZN A 801 1555 1555 1.98 LINK ZN ZN A 801 O1 ATSN A 802 1555 1555 2.03 LINK ZN ZN A 801 N1 ATSN A 802 1555 1555 2.65 LINK ZN ZN A 801 O1 BTSN A 802 1555 1555 1.80 LINK ZN ZN A 801 O2 ATSN A 802 1555 1555 2.21 LINK ZN ZN A 801 N1 BTSN A 802 1555 1555 2.32 LINK K K A 804 O HOH A1036 1555 1555 2.68 LINK K K A 804 O HOH A1061 1555 1555 2.94 LINK MG MG A 822 O HOH A 906 1555 1555 2.10 LINK MG MG A 822 O HOH A 966 1555 1555 2.14 LINK MG MG A 822 O HOH A1012 1555 1555 2.27 LINK MG MG A 822 O HOH A1041 1555 1555 2.16 LINK MG MG A 822 O HOH A1216 1555 1555 2.06 LINK MG MG A 822 O HOH A1298 1555 1555 2.06 CISPEP 1 ARG A 569 PRO A 570 0 -8.37 CISPEP 2 PHE A 643 PRO A 644 0 9.49 SITE 1 AC1 4 ASP A 612 HIS A 614 ASP A 705 TSN A 802 SITE 1 AC2 15 HIS A 463 PRO A 464 HIS A 573 HIS A 574 SITE 2 AC2 15 GLY A 582 PHE A 583 ASP A 612 HIS A 614 SITE 3 AC2 15 PHE A 643 ASP A 705 LEU A 712 GLY A 743 SITE 4 AC2 15 TYR A 745 ZN A 801 HOH A 921 SITE 1 AC3 5 ASP A 610 ASP A 612 HIS A 614 SER A 633 SITE 2 AC3 5 LEU A 634 SITE 1 AC4 6 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 2 AC4 6 HOH A1036 HOH A1061 SITE 1 AC5 2 ARG A 451 THR A 540 SITE 1 AC6 4 ARG A 481 LEU A 483 SER A 484 HOH A1279 SITE 1 AC7 4 PRO A 519 ARG A 520 HOH A1018 HOH A1211 SITE 1 AC8 5 TYR A 529 SER A 531 HOH A 928 HOH A 941 SITE 2 AC8 5 HOH A1123 SITE 1 AC9 5 ASP A 521 ARG A 524 LEU A 525 GLU A 528 SITE 2 AC9 5 HOH A1196 SITE 1 AD1 8 ASN A 457 SER A 461 LEU A 466 ARG A 660 SITE 2 AD1 8 HOH A 905 HOH A1074 HOH A1162 HOH A1247 SITE 1 AD2 5 ILE A 622 HOH A 908 HOH A 931 HOH A 938 SITE 2 AD2 5 HOH A1082 SITE 1 AD3 9 ASN A 436 ALA A 500 HIS A 503 SER A 504 SITE 2 AD3 9 SER A 505 ILE A 508 HOH A1097 HOH A1163 SITE 3 AD3 9 HOH A1273 SITE 1 AD4 8 ARG A 594 GLN A 597 GLU A 602 MG A 822 SITE 2 AD4 8 HOH A 906 HOH A 912 HOH A 966 HOH A1012 SITE 1 AD5 7 ARG A 492 THR A 495 GLU A 498 HOH A 903 SITE 2 AD5 7 HOH A 944 HOH A1016 HOH A1050 SITE 1 AD6 1 HOH A 944 SITE 1 AD7 3 THR A 558 GLY A 559 HOH A1022 SITE 1 AD8 7 ARG A 472 THR A 748 ALA A 791 PRO A 792 SITE 2 AD8 7 ARG A 798 HOH A 993 HOH A1039 SITE 1 AD9 9 SER A 471 SER A 475 PRO A 792 PHE A 793 SITE 2 AD9 9 SER A 795 ARG A 798 GOL A 819 HOH A1209 SITE 3 AD9 9 HOH A1253 SITE 1 AE1 5 ARG A 660 TYR A 662 PHE A 793 TRP A 794 SITE 2 AE1 5 GOL A 818 SITE 1 AE2 5 TRP A 459 PRO A 519 ASN A 523 HIS A 683 SITE 2 AE2 5 HOH A1111 SITE 1 AE3 6 ASN A 457 HIS A 463 SER A 531 ILE A 532 SITE 2 AE3 6 PHE A 583 HOH A 928 SITE 1 AE4 7 EDO A 813 HOH A 906 HOH A 966 HOH A1012 SITE 2 AE4 7 HOH A1041 HOH A1216 HOH A1298 CRYST1 48.439 69.639 50.193 90.00 110.42 90.00 P 1 21 1 2 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 0.020645 0.000000 0.007687 0.00000 SCALE2 0.000000 0.014360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021259 0.00000