HEADER HYDROLASE 25-NOV-20 7KUT TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 H137A MUTANT TITLE 2 IN COMPLEX WITH N-ACETYLPUTRESCINE (TETRAHEDRAL INTERMEDIATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYAMINE DEACETYLASE HDAC10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEACETYLASE 10; COMPND 5 EC: 3.5.1.48,3.5.1.62; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEACETYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HERBST-GERVASONI,D.W.CHRISTIANSON REVDAT 3 18-OCT-23 7KUT 1 REMARK REVDAT 2 17-FEB-21 7KUT 1 JRNL REVDAT 1 03-FEB-21 7KUT 0 JRNL AUTH C.J.HERBST-GERVASONI,D.W.CHRISTIANSON JRNL TITL X-RAY CRYSTALLOGRAPHIC SNAPSHOTS OF SUBSTRATE BINDING IN THE JRNL TITL 2 ACTIVE SITE OF HISTONE DEACETYLASE 10. JRNL REF BIOCHEMISTRY V. 60 303 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 33449614 JRNL DOI 10.1021/ACS.BIOCHEM.0C00936 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58703 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2883 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 60.5000 - 5.6500 1.00 2895 156 0.1744 0.2005 REMARK 3 2 5.6500 - 4.4900 1.00 2727 154 0.1502 0.2075 REMARK 3 3 4.4900 - 3.9200 1.00 2703 147 0.1446 0.1824 REMARK 3 4 3.9200 - 3.5600 1.00 2707 136 0.1496 0.1859 REMARK 3 5 3.5600 - 3.3100 1.00 2658 157 0.1656 0.2019 REMARK 3 6 3.3100 - 3.1100 1.00 2679 115 0.1797 0.2136 REMARK 3 7 3.1100 - 2.9600 1.00 2654 133 0.1839 0.2106 REMARK 3 8 2.9600 - 2.8300 1.00 2667 140 0.1793 0.2214 REMARK 3 9 2.8300 - 2.7200 1.00 2635 142 0.1828 0.2202 REMARK 3 10 2.7200 - 2.6300 1.00 2642 141 0.1897 0.2227 REMARK 3 11 2.6300 - 2.5400 1.00 2661 128 0.1996 0.2779 REMARK 3 12 2.5400 - 2.4700 1.00 2613 142 0.1948 0.2811 REMARK 3 13 2.4700 - 2.4100 1.00 2667 88 0.2006 0.2819 REMARK 3 14 2.4100 - 2.3500 1.00 2644 121 0.1970 0.2465 REMARK 3 15 2.3500 - 2.2900 1.00 2583 160 0.1954 0.2430 REMARK 3 16 2.2900 - 2.2400 1.00 2621 130 0.2029 0.2834 REMARK 3 17 2.2400 - 2.2000 1.00 2636 151 0.2128 0.2617 REMARK 3 18 2.2000 - 2.1600 1.00 2597 130 0.2250 0.2834 REMARK 3 19 2.1600 - 2.1200 1.00 2630 127 0.2327 0.2620 REMARK 3 20 2.1200 - 2.0800 1.00 2581 162 0.2440 0.3143 REMARK 3 21 2.0800 - 2.0500 1.00 2620 123 0.2560 0.3120 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) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.447 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.34 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 : 0.007 5060 REMARK 3 ANGLE : 0.858 6890 REMARK 3 CHIRALITY : 0.052 792 REMARK 3 PLANARITY : 0.005 884 REMARK 3 DIHEDRAL : 8.922 4075 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 7KUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000253198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-20 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) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58731 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 69.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.31700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 5TD7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC10, 10 MM REMARK 280 ACETYLPUTRESCINE, 1:1000 TRYPSIN:HDAC10, 0.113 M SODIUM REMARK 280 PHOSPHATE MONOBASIC, 0.068 M SODIUM PHOSPHATE DIBASIC, 18% REMARK 280 PEG3350 (W/V), 4% (V/V) POLYPROPYLENE GLYCOL P400, HDAC10 REMARK 280 MICROSEED, VAPOR 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 81.98667 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 163.97333 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 163.97333 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 81.98667 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 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 -1 REMARK 465 ASN A 0 REMARK 465 PRO A 369 REMARK 465 LYS A 370 REMARK 465 ARG A 371 REMARK 465 PRO A 372 REMARK 465 ARG A 373 REMARK 465 LEU A 374 REMARK 465 ASP A 375 REMARK 465 ALA A 376 REMARK 465 THR A 377 REMARK 465 ASN A 378 REMARK 465 GLY A 379 REMARK 465 GLY A 380 REMARK 465 PRO A 381 REMARK 465 LYS A 382 REMARK 465 GLU A 383 REMARK 465 SER A 384 REMARK 465 SER A 385 REMARK 465 GLU A 386 REMARK 465 PRO A 387 REMARK 465 ALA A 388 REMARK 465 SER A 389 REMARK 465 GLU A 390 REMARK 465 SER A 391 REMARK 465 ASN A 392 REMARK 465 PRO A 393 REMARK 465 LYS A 394 REMARK 465 LYS A 395 REMARK 465 THR A 396 REMARK 465 ALA A 397 REMARK 465 GLN A 398 REMARK 465 GLY A 435 REMARK 465 THR A 592 REMARK 465 ARG A 593 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 ARG A 41 CD NE CZ NH1 NH2 REMARK 470 GLN A 60 CD OE1 NE2 REMARK 470 GLU A 72 CD OE1 OE2 REMARK 470 LYS A 90 CE NZ REMARK 470 LYS A 220 CE NZ REMARK 470 LYS A 360 CG CD CE NZ REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 SER A 365 OG REMARK 470 GLU A 366 CG CD OE1 OE2 REMARK 470 THR A 367 OG1 CG2 REMARK 470 ASP A 399 CG OD1 OD2 REMARK 470 GLU A 404 CD OE1 OE2 REMARK 470 LYS A 407 CG CD CE NZ REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 THR A 426 OG1 CG2 REMARK 470 LYS A 429 CD CE NZ REMARK 470 ASP A 436 CG OD1 OD2 REMARK 470 GLU A 439 CG CD OE1 OE2 REMARK 470 LYS A 443 CG CD CE NZ REMARK 470 GLN A 446 CG CD OE1 NE2 REMARK 470 LYS A 451 CD CE NZ REMARK 470 HIS A 454 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 455 CG OD1 OD2 REMARK 470 LEU A 456 CG CD1 CD2 REMARK 470 GLN A 459 CG CD OE1 NE2 REMARK 470 ASN A 460 CG OD1 ND2 REMARK 470 ARG A 463 CG CD NE CZ NH1 NH2 REMARK 470 SER A 470 OG REMARK 470 ARG A 477 CG CD NE CZ NH1 NH2 REMARK 470 SER A 478 OG REMARK 470 ASP A 479 CG OD1 OD2 REMARK 470 GLU A 480 CG CD OE1 OE2 REMARK 470 GLU A 505 CG CD OE1 OE2 REMARK 470 GLU A 519 CG CD OE1 OE2 REMARK 470 LYS A 523 CE NZ REMARK 470 LYS A 537 CG CD CE NZ REMARK 470 GLU A 538 CG CD OE1 OE2 REMARK 470 GLU A 540 CG CD OE1 OE2 REMARK 470 LYS A 542 CG CD CE NZ REMARK 470 GLU A 553 CG CD OE1 OE2 REMARK 470 GLU A 555 CG CD OE1 OE2 REMARK 470 GLU A 587 CG CD OE1 OE2 REMARK 470 THR A 588 OG1 CG2 REMARK 470 LYS A 591 CG CD CE NZ REMARK 470 LEU A 594 CG CD1 CD2 REMARK 470 GLU A 626 CG CD OE1 OE2 REMARK 470 ARG A 644 CZ NH1 NH2 REMARK 470 LYS A 647 CE NZ REMARK 470 LYS A 656 CD CE NZ REMARK 470 GLU A 674 CG CD OE1 OE2 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 ARG A 15 46.54 -104.00 REMARK 500 ASP A 22 97.02 -166.32 REMARK 500 HIS A 197 144.37 -170.97 REMARK 500 VAL A 247 -64.00 -126.71 REMARK 500 GLU A 304 -107.30 -111.06 REMARK 500 THR A 457 -9.10 -145.31 REMARK 500 ASP A 458 105.70 -45.18 REMARK 500 PRO A 521 63.13 -69.92 REMARK 500 LEU A 568 -55.56 -125.83 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 K A 712 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 O REMARK 620 2 ASP A 172 OD2 69.4 REMARK 620 3 ASP A 174 O 93.6 96.3 REMARK 620 4 HIS A 176 O 163.3 94.5 83.7 REMARK 620 5 SER A 195 OG 90.6 114.5 148.3 100.4 REMARK 620 6 TRP A 196 O 88.3 155.0 73.2 106.5 75.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 711 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 174 OD2 REMARK 620 2 HIS A 176 ND1 108.1 REMARK 620 3 ASP A 267 OD2 113.7 96.2 REMARK 620 4 X51 A 702 O03 90.0 88.5 152.7 REMARK 620 5 X51 A 702 O04 138.5 97.0 95.1 57.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 713 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 185 O REMARK 620 2 ASP A 188 O 86.6 REMARK 620 3 VAL A 191 O 133.9 80.3 REMARK 620 4 PHE A 224 O 139.3 130.3 76.8 REMARK 620 5 HOH A 852 O 78.1 101.0 147.7 78.2 REMARK 620 6 HOH A1027 O 87.2 163.1 92.8 61.7 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 718 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 868 O REMARK 620 2 HOH A 940 O 78.2 REMARK 620 3 HOH A1035 O 71.2 79.1 REMARK 620 4 HOH A1055 O 144.2 81.8 76.1 REMARK 620 5 HOH A1106 O 93.6 70.2 148.1 107.1 REMARK 620 6 HOH A1112 O 80.6 156.6 103.3 121.5 101.5 REMARK 620 N 1 2 3 4 5 DBREF 7KUT A 2 675 UNP F1QCV2 HDA10_DANRE 2 675 SEQADV 7KUT SER A -1 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUT ASN A 0 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUT ALA A 1 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUT GLU A 24 UNP F1QCV2 ALA 24 CONFLICT SEQADV 7KUT ALA A 94 UNP F1QCV2 ASP 94 CONFLICT SEQADV 7KUT ALA A 137 UNP F1QCV2 HIS 137 ENGINEERED MUTATION SEQADV 7KUT PHE A 154 UNP F1QCV2 ILE 154 CONFLICT SEQADV 7KUT THR A 548 UNP F1QCV2 SER 548 CONFLICT SEQADV 7KUT GLU A 586 UNP F1QCV2 GLY 586 CONFLICT SEQADV 7KUT ARG A 593 UNP F1QCV2 GLY 593 CONFLICT SEQADV 7KUT ARG A 596 UNP F1QCV2 THR 596 CONFLICT SEQADV 7KUT MET A 613 UNP F1QCV2 THR 613 CONFLICT SEQADV 7KUT PRO A 646 UNP F1QCV2 LEU 646 CONFLICT SEQADV 7KUT TRP A 676 UNP F1QCV2 EXPRESSION TAG SEQRES 1 A 678 SER ASN ALA ALA SER GLY SER ALA LEU ILE PHE ASP GLU SEQRES 2 A 678 GLU MET SER ARG TYR LYS LEU LEU TRP THR ASP PRO GLU SEQRES 3 A 678 CYS GLU ILE GLU VAL PRO GLU ARG LEU THR VAL SER TYR SEQRES 4 A 678 GLU ALA LEU ARG THR HIS GLY LEU ALA GLN ARG CYS LYS SEQRES 5 A 678 ALA VAL PRO VAL ARG GLN ALA THR GLU GLN GLU ILE LEU SEQRES 6 A 678 LEU ALA HIS SER GLU GLU TYR LEU GLU ALA VAL LYS GLN SEQRES 7 A 678 THR PRO GLY MET ASN VAL GLU GLU LEU MET ALA PHE SER SEQRES 8 A 678 LYS LYS TYR ASN ALA VAL TYR PHE HIS GLN ASN ILE TYR SEQRES 9 A 678 HIS CYS ALA LYS LEU ALA ALA GLY ALA THR LEU GLN LEU SEQRES 10 A 678 VAL ASP SER VAL MET LYS ARG GLU VAL ARG ASN GLY MET SEQRES 11 A 678 ALA LEU VAL ARG PRO PRO GLY HIS ALA SER GLN ARG SER SEQRES 12 A 678 ALA ALA ASN GLY PHE CYS VAL PHE ASN ASN VAL ALA PHE SEQRES 13 A 678 ALA ALA LEU TYR ALA LYS LYS ASN TYR ASN LEU ASN ARG SEQRES 14 A 678 ILE LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY GLN GLY SEQRES 15 A 678 ILE GLN TYR CYS PHE GLU GLU ASP PRO SER VAL LEU TYR SEQRES 16 A 678 PHE SER TRP HIS ARG TYR GLU HIS GLN SER PHE TRP PRO SEQRES 17 A 678 ASN LEU PRO GLU SER ASP TYR SER SER VAL GLY LYS GLY SEQRES 18 A 678 LYS GLY SER GLY PHE ASN ILE ASN LEU PRO TRP ASN LYS SEQRES 19 A 678 VAL GLY MET THR ASN SER ASP TYR LEU ALA ALA PHE PHE SEQRES 20 A 678 HIS VAL LEU LEU PRO VAL ALA TYR GLU PHE ASP PRO GLU SEQRES 21 A 678 LEU VAL ILE VAL SER ALA GLY PHE ASP SER ALA ILE GLY SEQRES 22 A 678 ASP PRO GLU GLY GLU MET CYS ALA LEU PRO GLU ILE PHE SEQRES 23 A 678 ALA HIS LEU THR HIS LEU LEU MET PRO LEU ALA ALA GLY SEQRES 24 A 678 LYS MET CYS VAL VAL LEU GLU GLY GLY TYR ASN LEU THR SEQRES 25 A 678 SER LEU GLY GLN SER VAL CYS GLN THR VAL HIS SER LEU SEQRES 26 A 678 LEU GLY ASP PRO THR PRO ARG ILE SER GLY LEU GLY THR SEQRES 27 A 678 ALA CYS ASP SER ALA LEU GLU SER ILE GLN ASN VAL ARG SEQRES 28 A 678 ASN VAL GLN SER SER TYR TRP SER SER PHE LYS HIS LEU SEQRES 29 A 678 ALA GLN SER GLU THR ASN PRO LYS ARG PRO ARG LEU ASP SEQRES 30 A 678 ALA THR ASN GLY GLY PRO LYS GLU SER SER GLU PRO ALA SEQRES 31 A 678 SER GLU SER ASN PRO LYS LYS THR ALA GLN ASP ILE VAL SEQRES 32 A 678 TRP PRO GLU PRO LEU LYS ARG MET PRO ALA SER VAL ARG SEQRES 33 A 678 THR VAL VAL VAL PRO PRO PRO GLY VAL GLU LEU THR LEU SEQRES 34 A 678 PRO LYS ASN CYS GLN HIS SER GLY ASP ILE SER GLU SER SEQRES 35 A 678 THR ALA LYS GLU VAL GLN ARG ILE ARG ASP LYS HIS PHE SEQRES 36 A 678 HIS ASP LEU THR ASP GLN ASN ILE LEU ARG SER LEU GLY SEQRES 37 A 678 ASN ILE ILE SER VAL LEU ASP ARG MET MET ARG SER ASP SEQRES 38 A 678 GLU VAL CYS ASN GLY CYS VAL VAL VAL SER ASP LEU SER SEQRES 39 A 678 VAL SER VAL GLN CYS ALA LEU GLN HIS ALA LEU THR GLU SEQRES 40 A 678 PRO ALA GLU ARG VAL LEU VAL VAL TYR VAL GLY ASP GLY SEQRES 41 A 678 GLU LEU PRO VAL LYS THR ASN ASP GLY LYS VAL PHE LEU SEQRES 42 A 678 VAL GLN ILE CYS THR LYS GLU THR GLU ASP LYS CYS VAL SEQRES 43 A 678 ASN ARG LEU THR LEU CYS LEU ARG GLU GLY GLU SER LEU SEQRES 44 A 678 THR ALA GLY PHE MET GLN ALA LEU LEU GLY LEU ILE LEU SEQRES 45 A 678 PRO VAL ALA TYR GLU PHE ASN PRO ALA LEU VAL LEU GLY SEQRES 46 A 678 ILE VAL GLU GLU THR ALA ALA LYS THR ARG LEU MET ARG SEQRES 47 A 678 VAL TRP GLY HIS MET THR CYS LEU ILE GLN GLY LEU ALA SEQRES 48 A 678 ARG GLY ARG MET LEU THR LEU LEU GLN GLY TYR ASP LYS SEQRES 49 A 678 ASP LEU LEU GLU LEU THR VAL SER ALA LEU SER GLY ALA SEQRES 50 A 678 SER ILE SER PRO LEU GLY PRO LEU ARG ALA PRO LYS PRO SEQRES 51 A 678 GLU ASP VAL GLU MET MET GLU LYS GLN ARG GLN ARG LEU SEQRES 52 A 678 GLN GLU ARG TRP GLY LEU LEU ARG CYS THR VAL SER GLU SEQRES 53 A 678 SER TRP HET EDO A 701 4 HET X51 A 702 10 HET PEG A 703 7 HET PEG A 704 7 HET EDO A 705 4 HET EDO A 706 4 HET EDO A 707 4 HET EDO A 708 4 HET EDO A 709 4 HET EDO A 710 4 HET ZN A 711 1 HET K A 712 1 HET K A 713 1 HET PO4 A 714 5 HET PO4 A 715 5 HET PO4 A 716 5 HET PO4 A 717 5 HET NA A 718 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM X51 1-[(4-AMINOBUTYL)AMINO]ETHANE-1,1-DIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 7(C2 H6 O2) FORMUL 3 X51 C6 H16 N2 O2 FORMUL 4 PEG 2(C4 H10 O3) FORMUL 12 ZN ZN 2+ FORMUL 13 K 2(K 1+) FORMUL 15 PO4 4(O4 P 3-) FORMUL 19 NA NA 1+ FORMUL 20 HOH *329(H2 O) HELIX 1 AA1 ASP A 10 ARG A 15 5 6 HELIX 2 AA2 PRO A 30 HIS A 43 1 14 HELIX 3 AA3 LEU A 45 CYS A 49 5 5 HELIX 4 AA4 THR A 58 LEU A 63 1 6 HELIX 5 AA5 SER A 67 GLN A 76 1 10 HELIX 6 AA6 THR A 77 MET A 80 5 4 HELIX 7 AA7 ASN A 81 LYS A 91 1 11 HELIX 8 AA8 ASN A 100 LYS A 121 1 22 HELIX 9 AA9 ASN A 150 ASN A 164 1 15 HELIX 10 AB1 GLY A 178 GLU A 186 1 9 HELIX 11 AB2 LEU A 208 ASP A 212 5 5 HELIX 12 AB3 LYS A 218 SER A 222 5 5 HELIX 13 AB4 THR A 236 VAL A 247 1 12 HELIX 14 AB5 VAL A 247 ASP A 256 1 10 HELIX 15 AB6 GLY A 265 ALA A 269 5 5 HELIX 16 AB7 PRO A 281 MET A 292 1 12 HELIX 17 AB8 PRO A 293 GLY A 297 5 5 HELIX 18 AB9 ASN A 308 LEU A 324 1 17 HELIX 19 AC1 CYS A 338 SER A 353 1 16 HELIX 20 AC2 TRP A 356 HIS A 361 1 6 HELIX 21 AC3 LEU A 362 GLN A 364 5 3 HELIX 22 AC4 SER A 438 PHE A 453 1 16 HELIX 23 AC5 ASP A 458 ARG A 477 1 20 HELIX 24 AC6 ASP A 490 LEU A 503 1 14 HELIX 25 AC7 SER A 556 LEU A 568 1 13 HELIX 26 AC8 LEU A 568 ASN A 577 1 10 HELIX 27 AC9 GLU A 587 ALA A 590 5 4 HELIX 28 AD1 VAL A 597 GLN A 606 1 10 HELIX 29 AD2 GLY A 607 GLY A 611 5 5 HELIX 30 AD3 ASP A 621 SER A 633 1 13 HELIX 31 AD4 LYS A 647 GLN A 662 1 16 HELIX 32 AD5 TRP A 665 ARG A 669 5 5 SHEET 1 AA1 8 LYS A 50 VAL A 52 0 SHEET 2 AA1 8 SER A 5 ILE A 8 1 N SER A 5 O LYS A 50 SHEET 3 AA1 8 ASN A 126 ALA A 129 1 O MET A 128 N ILE A 8 SHEET 4 AA1 8 MET A 299 LEU A 303 1 O VAL A 301 N GLY A 127 SHEET 5 AA1 8 LEU A 259 ALA A 264 1 N VAL A 262 O VAL A 302 SHEET 6 AA1 8 ILE A 168 ASP A 172 1 N LEU A 169 O ILE A 261 SHEET 7 AA1 8 VAL A 191 ARG A 198 1 O LEU A 192 N ILE A 170 SHEET 8 AA1 8 ASN A 225 TRP A 230 1 O TRP A 230 N HIS A 197 SHEET 1 AA2 8 CYS A 431 HIS A 433 0 SHEET 2 AA2 8 VAL A 413 VAL A 418 1 N VAL A 417 O GLN A 432 SHEET 3 AA2 8 VAL A 481 VAL A 488 1 O ASN A 483 N ARG A 414 SHEET 4 AA2 8 MET A 613 GLN A 618 1 O LEU A 617 N VAL A 488 SHEET 5 AA2 8 LEU A 580 VAL A 585 1 N GLY A 583 O LEU A 616 SHEET 6 AA2 8 VAL A 510 VAL A 515 1 N LEU A 511 O LEU A 582 SHEET 7 AA2 8 VAL A 529 CYS A 535 1 O VAL A 532 N VAL A 512 SHEET 8 AA2 8 ARG A 546 CYS A 550 1 O LEU A 549 N GLN A 533 SSBOND 1 CYS A 543 CYS A 543 1555 4555 2.08 LINK O ASP A 172 K K A 712 1555 1555 2.87 LINK OD2 ASP A 172 K K A 712 1555 1555 2.77 LINK OD2 ASP A 174 ZN ZN A 711 1555 1555 1.86 LINK O ASP A 174 K K A 712 1555 1555 2.61 LINK ND1 HIS A 176 ZN ZN A 711 1555 1555 2.17 LINK O HIS A 176 K K A 712 1555 1555 2.65 LINK O PHE A 185 K K A 713 1555 1555 2.58 LINK O ASP A 188 K K A 713 1555 1555 2.66 LINK O VAL A 191 K K A 713 1555 1555 2.45 LINK OG SER A 195 K K A 712 1555 1555 2.76 LINK O TRP A 196 K K A 712 1555 1555 2.62 LINK O PHE A 224 K K A 713 1555 1555 3.24 LINK OD2 ASP A 267 ZN ZN A 711 1555 1555 2.03 LINK O03 X51 A 702 ZN ZN A 711 1555 1555 2.57 LINK O04 X51 A 702 ZN ZN A 711 1555 1555 2.11 LINK K K A 713 O HOH A 852 1555 1555 2.61 LINK K K A 713 O HOH A1027 1555 1555 2.27 LINK NA NA A 718 O HOH A 868 1555 1555 2.66 LINK NA NA A 718 O HOH A 940 1555 1555 3.08 LINK NA NA A 718 O HOH A1035 1555 1555 2.81 LINK NA NA A 718 O HOH A1055 1555 1555 2.58 LINK NA NA A 718 O HOH A1106 1555 1555 3.00 LINK NA NA A 718 O HOH A1112 1555 1555 2.46 CISPEP 1 ARG A 132 PRO A 133 0 -2.08 CISPEP 2 TRP A 205 PRO A 206 0 6.31 CISPEP 3 GLU A 505 PRO A 506 0 -2.22 CRYST1 80.248 80.248 245.960 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 0.012461 0.007195 0.000000 0.00000 SCALE2 0.000000 0.014389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004066 0.00000