HEADER HYDROLASE 25-NOV-20 7KUQ TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 Y307F MUTANT TITLE 2 IN COMPLEX WITH N8-ACETYLSPERMIDINE 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 7KUQ 1 REMARK REVDAT 2 17-FEB-21 7KUQ 1 JRNL REVDAT 1 03-FEB-21 7KUQ 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 55697 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2832 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 60.8500 - 5.7000 0.99 2858 163 0.1736 0.2018 REMARK 3 2 5.7000 - 4.5200 1.00 2768 122 0.1723 0.1832 REMARK 3 3 4.5200 - 3.9500 1.00 2696 126 0.1660 0.2181 REMARK 3 4 3.9500 - 3.5900 1.00 2716 110 0.1853 0.2448 REMARK 3 5 3.5900 - 3.3300 0.99 2603 175 0.1976 0.2428 REMARK 3 6 3.3300 - 3.1400 0.99 2649 123 0.2153 0.2572 REMARK 3 7 3.1400 - 2.9800 1.00 2634 130 0.2103 0.2379 REMARK 3 8 2.9800 - 2.8500 1.00 2639 146 0.2085 0.2501 REMARK 3 9 2.8500 - 2.7400 1.00 2628 149 0.2130 0.2848 REMARK 3 10 2.7400 - 2.6500 1.00 2624 150 0.2257 0.2412 REMARK 3 11 2.6500 - 2.5600 1.00 2606 139 0.2300 0.2571 REMARK 3 12 2.5600 - 2.4900 1.00 2641 117 0.2341 0.3094 REMARK 3 13 2.4900 - 2.4200 1.00 2595 166 0.2360 0.3091 REMARK 3 14 2.4200 - 2.3700 1.00 2613 111 0.2403 0.2875 REMARK 3 15 2.3700 - 2.3100 1.00 2637 162 0.2466 0.2746 REMARK 3 16 2.3100 - 2.2600 1.00 2593 130 0.2547 0.2761 REMARK 3 17 2.2600 - 2.2200 1.00 2565 165 0.2765 0.3311 REMARK 3 18 2.2200 - 2.1800 1.00 2598 124 0.2907 0.3288 REMARK 3 19 2.1800 - 2.1400 1.00 2640 166 0.2898 0.3502 REMARK 3 20 2.1400 - 2.1000 1.00 2562 158 0.2996 0.3279 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.989 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.20 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 4981 REMARK 3 ANGLE : 0.926 6783 REMARK 3 CHIRALITY : 0.052 780 REMARK 3 PLANARITY : 0.006 872 REMARK 3 DIHEDRAL : 9.398 4038 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 7KUQ 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_1000253189. 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 : 55699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 69.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.21700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.13600 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 (%): 60.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC10, 10 MM N8 REMARK 280 -ACETYLSPERMIDINE, 1:1000 TRYPSIN:HDAC10, 0.125 M SODIUM REMARK 280 PHOSPHATE DIBASIC, 0.075 M SODIUM PHOSPHATE MONOBASIC, 20% REMARK 280 PEG3350 (W/V), HDAC10 MICROSEED, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 83.12667 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 166.25333 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 166.25333 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 83.12667 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 ALA A 589 REMARK 465 ALA A 590 REMARK 465 LYS A 591 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 GLU A 72 CD OE1 OE2 REMARK 470 LYS A 360 CG CD CE NZ REMARK 470 GLN A 364 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 LYS A 407 CD CE NZ REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 ASP A 436 CG OD1 OD2 REMARK 470 GLU A 439 OE1 OE2 REMARK 470 LYS A 443 CG CD CE NZ REMARK 470 GLU A 444 CG CD OE1 OE2 REMARK 470 GLN A 446 CG CD OE1 NE2 REMARK 470 ASP A 450 CG OD1 OD2 REMARK 470 LYS A 451 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 ARG A 463 NE CZ NH1 NH2 REMARK 470 ARG A 477 CG CD NE CZ NH1 NH2 REMARK 470 SER A 478 OG REMARK 470 GLU A 480 CG CD OE1 OE2 REMARK 470 ASP A 490 OD1 OD2 REMARK 470 GLU A 505 CG CD OE1 OE2 REMARK 470 GLU A 508 CG CD OE1 OE2 REMARK 470 GLU A 519 OE1 OE2 REMARK 470 LYS A 523 CG CD CE NZ REMARK 470 LYS A 528 CD 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 ASP A 541 CG OD1 OD2 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 LEU A 594 CD1 CD2 REMARK 470 ARG A 596 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 610 CZ NH1 NH2 REMARK 470 LYS A 622 CG CD CE NZ REMARK 470 ILE A 637 CD1 REMARK 470 ARG A 644 CZ NH1 NH2 REMARK 470 LYS A 647 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 41.35 -108.26 REMARK 500 ASP A 22 97.98 -169.28 REMARK 500 PHE A 146 -1.82 68.01 REMARK 500 TYR A 199 -49.60 -134.21 REMARK 500 GLN A 202 3.38 80.78 REMARK 500 VAL A 247 -66.17 -127.40 REMARK 500 GLU A 304 -104.97 -111.25 REMARK 500 LYS A 451 -60.41 -90.84 REMARK 500 ASP A 455 34.55 -80.80 REMARK 500 ASN A 525 50.46 -113.18 REMARK 500 ASP A 526 -1.43 -160.40 REMARK 500 LEU A 568 -56.44 -126.97 REMARK 500 MET A 595 -61.08 58.18 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 703 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 O REMARK 620 2 ASP A 172 OD2 73.0 REMARK 620 3 ASP A 174 O 94.8 95.9 REMARK 620 4 HIS A 176 O 170.5 97.7 84.6 REMARK 620 5 SER A 195 OG 86.6 119.2 143.3 99.6 REMARK 620 6 TRP A 196 O 88.2 158.0 74.0 100.7 69.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 174 OD1 REMARK 620 2 ASP A 174 OD2 56.5 REMARK 620 3 HIS A 176 ND1 162.8 107.0 REMARK 620 4 ASP A 267 OD2 86.7 107.5 94.7 REMARK 620 5 Q9C A 701 O 101.2 145.0 95.8 96.4 REMARK 620 6 HOH A 808 O 86.8 83.5 96.8 161.0 67.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 704 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 185 O REMARK 620 2 ASP A 188 O 95.4 REMARK 620 3 VAL A 191 O 146.9 81.9 REMARK 620 4 HOH A 873 O 85.1 107.1 127.3 REMARK 620 5 HOH A 908 O 94.3 163.2 82.5 87.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 708 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 811 O REMARK 620 2 HOH A 833 O 86.0 REMARK 620 3 HOH A 871 O 88.2 91.6 REMARK 620 4 HOH A 965 O 175.4 91.1 95.4 REMARK 620 5 HOH A 976 O 85.7 166.6 77.6 97.8 REMARK 620 N 1 2 3 4 DBREF 7KUQ A 2 675 UNP F1QCV2 HDA10_DANRE 2 675 SEQADV 7KUQ SER A -1 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUQ ASN A 0 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUQ ALA A 1 UNP F1QCV2 EXPRESSION TAG SEQADV 7KUQ GLU A 24 UNP F1QCV2 ALA 24 CONFLICT SEQADV 7KUQ ALA A 94 UNP F1QCV2 ASP 94 CONFLICT SEQADV 7KUQ PHE A 154 UNP F1QCV2 ILE 154 CONFLICT SEQADV 7KUQ PHE A 307 UNP F1QCV2 TYR 307 ENGINEERED MUTATION SEQADV 7KUQ THR A 548 UNP F1QCV2 SER 548 CONFLICT SEQADV 7KUQ GLU A 586 UNP F1QCV2 GLY 586 CONFLICT SEQADV 7KUQ ARG A 593 UNP F1QCV2 GLY 593 CONFLICT SEQADV 7KUQ ARG A 596 UNP F1QCV2 THR 596 CONFLICT SEQADV 7KUQ MET A 613 UNP F1QCV2 THR 613 CONFLICT SEQADV 7KUQ PRO A 646 UNP F1QCV2 LEU 646 CONFLICT SEQADV 7KUQ 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 HIS 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 PHE 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 Q9C A 701 13 HET ZN A 702 1 HET K A 703 1 HET K A 704 1 HET PO4 A 705 5 HET PO4 A 706 5 HET PO4 A 707 5 HET NA A 708 1 HETNAM Q9C N-{4-[(3-AMINOPROPYL)AMINO]BUTYL}ACETAMIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETSYN Q9C N8-ACETYLSPERMIDINE FORMUL 2 Q9C C9 H21 N3 O FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 PO4 3(O4 P 3-) FORMUL 9 NA NA 1+ FORMUL 10 HOH *184(H2 O) HELIX 1 AA1 GLU A 11 ARG A 15 5 5 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 90 1 10 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 GLU A 282 MET A 292 1 11 HELIX 16 AB7 PRO A 293 GLY A 297 5 5 HELIX 17 AB8 ASN A 308 LEU A 324 1 17 HELIX 18 AB9 CYS A 338 SER A 353 1 16 HELIX 19 AC1 SER A 354 TYR A 355 5 2 HELIX 20 AC2 TRP A 356 GLN A 364 5 9 HELIX 21 AC3 SER A 438 PHE A 453 1 16 HELIX 22 AC4 LEU A 462 SER A 478 1 17 HELIX 23 AC5 ASP A 490 THR A 504 1 15 HELIX 24 AC6 SER A 556 LEU A 568 1 13 HELIX 25 AC7 LEU A 568 ASN A 577 1 10 HELIX 26 AC8 VAL A 597 GLN A 606 1 10 HELIX 27 AC9 GLY A 607 GLY A 611 5 5 HELIX 28 AD1 ASP A 621 SER A 633 1 13 HELIX 29 AD2 LYS A 647 GLN A 662 1 16 HELIX 30 AD3 TRP A 665 ARG A 669 5 5 SHEET 1 AA1 8 LYS A 50 ALA A 51 0 SHEET 2 AA1 8 SER A 5 PHE A 9 1 N LEU A 7 O LYS A 50 SHEET 3 AA1 8 ASN A 126 LEU A 130 1 O LEU A 130 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 VAL A 171 O SER A 263 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 THR A 615 N VAL A 486 SHEET 5 AA2 8 LEU A 580 VAL A 585 1 N VAL A 581 O LEU A 614 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 547 N GLN A 533 SSBOND 1 CYS A 543 CYS A 543 1555 4555 2.08 LINK O ASP A 172 K K A 703 1555 1555 2.92 LINK OD2 ASP A 172 K K A 703 1555 1555 2.72 LINK OD1 ASP A 174 ZN ZN A 702 1555 1555 2.62 LINK OD2 ASP A 174 ZN ZN A 702 1555 1555 1.96 LINK O ASP A 174 K K A 703 1555 1555 2.70 LINK ND1 HIS A 176 ZN ZN A 702 1555 1555 2.36 LINK O HIS A 176 K K A 703 1555 1555 2.69 LINK O PHE A 185 K K A 704 1555 1555 2.44 LINK O ASP A 188 K K A 704 1555 1555 2.40 LINK O VAL A 191 K K A 704 1555 1555 2.60 LINK OG SER A 195 K K A 703 1555 1555 2.80 LINK O TRP A 196 K K A 703 1555 1555 2.68 LINK OD2 ASP A 267 ZN ZN A 702 1555 1555 1.96 LINK O Q9C A 701 ZN ZN A 702 1555 1555 2.21 LINK ZN ZN A 702 O HOH A 808 1555 1555 2.20 LINK K K A 704 O HOH A 873 1555 1555 2.52 LINK K K A 704 O HOH A 908 1555 1555 2.29 LINK NA NA A 708 O HOH A 811 1555 1555 2.67 LINK NA NA A 708 O HOH A 833 1555 1555 2.62 LINK NA NA A 708 O HOH A 871 1555 1555 2.62 LINK NA NA A 708 O HOH A 965 1555 1555 2.48 LINK NA NA A 708 O HOH A 976 1555 1555 2.78 CISPEP 1 ARG A 132 PRO A 133 0 -3.01 CISPEP 2 TRP A 205 PRO A 206 0 4.28 CISPEP 3 GLU A 505 PRO A 506 0 -6.58 CRYST1 80.509 80.509 249.380 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 0.012421 0.007171 0.000000 0.00000 SCALE2 0.000000 0.014343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004010 0.00000