HEADER HYDROLASE/INHIBITOR 06-AUG-23 8TQ0 TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 COMPLEXED WITH (R)-LIPOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2; 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 HYDROLASE, HISTONE DEACETYLASE, INHIBITOR, METALLOHYDROLASE, KEYWDS 2 HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.R.WATSON,D.W.CHRISTIANSON REVDAT 3 03-APR-24 8TQ0 1 JRNL REVDAT 2 04-OCT-23 8TQ0 1 TITLE REVDAT 1 20-SEP-23 8TQ0 0 JRNL AUTH P.R.WATSON,J.G.STOLLMAIER,D.W.CHRISTIANSON JRNL TITL CRYSTAL STRUCTURE OF HISTONE DEACETYLASE 6 COMPLEXED WITH JRNL TITL 2 (R)-LIPOIC ACID, AN ESSENTIAL COFACTOR IN CENTRAL CARBON JRNL TITL 3 METABOLISM. JRNL REF J.BIOL.CHEM. V. 299 05228 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37703993 JRNL DOI 10.1016/J.JBC.2023.105228 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.520 REMARK 3 FREE R VALUE TEST SET COUNT : 3731 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 29.6000 - 7.1700 0.99 1716 146 0.1610 0.2141 REMARK 3 2 7.1600 - 5.7000 1.00 1727 134 0.1862 0.2191 REMARK 3 3 5.7000 - 4.9900 1.00 1733 146 0.1632 0.1575 REMARK 3 4 4.9900 - 4.5300 1.00 1730 141 0.1512 0.1689 REMARK 3 5 4.5300 - 4.2100 1.00 1704 144 0.1451 0.1507 REMARK 3 6 4.2100 - 3.9600 1.00 1744 133 0.1591 0.2113 REMARK 3 7 3.9600 - 3.7600 0.86 1490 130 0.2327 0.2321 REMARK 3 8 3.7600 - 3.6000 0.82 1399 111 0.2246 0.2524 REMARK 3 9 3.6000 - 3.4600 0.95 1669 130 0.2158 0.2686 REMARK 3 10 3.4600 - 3.3400 0.98 1692 135 0.2264 0.3061 REMARK 3 11 3.3400 - 3.2400 1.00 1721 136 0.2215 0.2866 REMARK 3 12 3.2400 - 3.1400 1.00 1737 140 0.2207 0.2693 REMARK 3 13 3.1400 - 3.0600 1.00 1743 131 0.2233 0.3038 REMARK 3 14 3.0600 - 2.9900 1.00 1692 141 0.2215 0.2502 REMARK 3 15 2.9900 - 2.9200 1.00 1788 136 0.2237 0.2349 REMARK 3 16 2.9200 - 2.8600 1.00 1711 145 0.2287 0.2595 REMARK 3 17 2.8600 - 2.8000 1.00 1701 156 0.2254 0.3125 REMARK 3 18 2.8000 - 2.7500 1.00 1740 119 0.2335 0.2402 REMARK 3 19 2.7500 - 2.7000 1.00 1692 154 0.2334 0.2603 REMARK 3 20 2.7000 - 2.6500 0.97 1743 122 0.2687 0.3464 REMARK 3 21 2.6500 - 2.6100 0.98 1672 137 0.2392 0.3540 REMARK 3 22 2.6100 - 2.5700 1.00 1723 152 0.2130 0.2853 REMARK 3 23 2.5700 - 2.5300 1.00 1736 145 0.2382 0.2550 REMARK 3 24 2.5300 - 2.5000 0.99 1720 118 0.2298 0.3010 REMARK 3 25 2.5000 - 2.4600 1.00 1741 155 0.2257 0.2896 REMARK 3 26 2.4600 - 2.4300 1.00 1680 145 0.2319 0.2688 REMARK 3 27 2.4300 - 2.4000 1.00 1737 149 0.2386 0.3737 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.276 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.924 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.19 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 : 0.003 5567 REMARK 3 ANGLE : 0.554 7566 REMARK 3 CHIRALITY : 0.042 840 REMARK 3 PLANARITY : 0.004 983 REMARK 3 DIHEDRAL : 7.713 771 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 442 through 450 or REMARK 3 resid 452 through 458 or resid 460 REMARK 3 through 478 or (resid 479 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 480 through 505 or (resid 506 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB or name CG )) or resid 507 REMARK 3 through 576 or (resid 577 through 578 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 579 through 671 or REMARK 3 (resid 672 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 673 through 719 or (resid 720 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 721 through 748 or REMARK 3 resid 750 through 754 or resid 756 REMARK 3 through 770 or resid 774 through 775 or REMARK 3 (resid 776 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 777 REMARK 3 through 797 or (resid 801 and (name C02 REMARK 3 or name C03 or name C04 or name C05 or REMARK 3 name C06 or name C07 or name C08 or name REMARK 3 S01 or name S12)))) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 442 through 450 or REMARK 3 resid 452 through 458 or resid 460 REMARK 3 through 477 or (resid 478 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 479 through 514 or REMARK 3 (resid 515 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 516 REMARK 3 through 519 or (resid 520 through 521 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 522 through 523 or REMARK 3 (resid 524 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 525 REMARK 3 through 561 or (resid 562 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 563 through 657 or REMARK 3 (resid 658 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 659 through 748 or resid 750 REMARK 3 through 754 or resid 756 through 797 or REMARK 3 resid 801)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8TQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-23 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26674 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.21800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC6, 0.2 M POTASSIUM REMARK 280 CITRATE TRIBASIC AND 20% (W/V) POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 37.44700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.33300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.33300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.44700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.07800 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 435 REMARK 465 ASN A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 GLY A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 HIS A 771 REMARK 465 LEU A 772 REMARK 465 ARG A 798 REMARK 465 SER B 435 REMARK 465 ASN B 436 REMARK 465 ALA B 437 REMARK 465 GLY B 438 REMARK 465 GLY B 439 REMARK 465 SER B 440 REMARK 465 SER B 441 REMARK 465 HIS B 771 REMARK 465 LEU B 772 REMARK 465 THR B 773 REMARK 465 ARG B 798 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 478 CD OE1 OE2 REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 GLU A 515 CG CD OE1 OE2 REMARK 470 LYS A 518 CG CD CE NZ REMARK 470 ARG A 520 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 521 CG OD1 OD2 REMARK 470 ARG A 524 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 562 CD NE CZ NH1 NH2 REMARK 470 GLU A 602 CG CD OE1 OE2 REMARK 470 LYS A 658 CD CE NZ REMARK 470 ARG A 736 NE CZ NH1 NH2 REMARK 470 ASP A 770 CG OD1 OD2 REMARK 470 ARG A 788 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 479 CG CD OE1 OE2 REMARK 470 GLU B 497 CG CD OE1 OE2 REMARK 470 LYS B 506 CD CE NZ REMARK 470 LYS B 518 CG CD CE NZ REMARK 470 ARG B 562 NE CZ NH1 NH2 REMARK 470 LYS B 577 CG CD CE NZ REMARK 470 ASP B 578 CG OD1 OD2 REMARK 470 GLU B 602 CG CD OE1 OE2 REMARK 470 LYS B 658 CE NZ REMARK 470 LYS B 672 CD CE NZ REMARK 470 GLU B 720 CG CD OE1 OE2 REMARK 470 ARG B 736 NE CZ NH1 NH2 REMARK 470 ASP B 770 CG OD1 OD2 REMARK 470 LYS B 776 CG CD CE NZ REMARK 470 ARG B 788 CG CD NE CZ NH1 NH2 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 68.22 62.03 REMARK 500 PRO A 571 -177.90 -67.67 REMARK 500 THR A 600 -93.79 -127.44 REMARK 500 LEU A 685 -59.28 -125.21 REMARK 500 GLN A 716 42.53 -140.99 REMARK 500 GLU A 742 -110.19 -119.72 REMARK 500 SER B 531 68.56 62.81 REMARK 500 PRO B 571 -177.75 -68.21 REMARK 500 THR B 600 -93.76 -127.22 REMARK 500 ASN B 669 -32.87 -130.79 REMARK 500 LEU B 685 -59.53 -124.74 REMARK 500 GLN B 716 43.14 -143.31 REMARK 500 GLU B 742 -111.00 -119.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 RED B 801 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 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 69.7 REMARK 620 3 ASP A 612 O 100.2 91.5 REMARK 620 4 HIS A 614 O 159.2 89.7 76.4 REMARK 620 5 SER A 633 OG 81.8 110.2 157.2 109.4 REMARK 620 6 LEU A 634 O 75.0 134.3 67.0 120.6 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 106.1 REMARK 620 3 ASP A 705 OD2 105.4 100.9 REMARK 620 4 RED A 801 S8 117.0 113.3 112.6 REMARK 620 N 1 2 3 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 PHE A 623 O REMARK 620 2 ASP A 626 O 79.5 REMARK 620 3 VAL A 629 O 116.8 80.0 REMARK 620 4 TYR A 662 O 153.7 115.8 87.9 REMARK 620 5 HOH A 914 O 80.2 84.9 154.3 80.1 REMARK 620 6 HOH A 936 O 65.8 145.2 117.5 95.6 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 71.1 REMARK 620 3 ASP B 612 O 100.3 94.3 REMARK 620 4 HIS B 614 O 161.5 90.9 76.5 REMARK 620 5 SER B 633 OG 80.4 110.8 153.3 110.8 REMARK 620 6 LEU B 634 O 74.1 135.2 65.2 119.2 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 109.9 REMARK 620 3 ASP B 705 OD2 106.0 95.0 REMARK 620 4 RED B 801 S8 119.9 107.0 116.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 81.8 REMARK 620 3 VAL B 629 O 119.9 83.0 REMARK 620 4 TYR B 662 O 155.5 111.7 82.9 REMARK 620 5 HOH B 917 O 82.8 86.0 152.8 78.1 REMARK 620 6 HOH B 929 O 66.9 146.7 121.9 94.3 79.1 REMARK 620 N 1 2 3 4 5 DBREF 8TQ0 A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 8TQ0 B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 8TQ0 SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 GLY A 439 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 8TQ0 GLY B 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 SEQRES 1 B 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 B 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 B 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 B 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 B 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 B 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 B 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 B 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 B 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 B 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 B 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 B 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 B 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 B 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 B 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 B 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 B 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 B 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 B 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 B 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 B 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 B 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 B 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 B 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 B 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 B 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 B 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 B 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG HET RED A 801 12 HET ZN A 802 1 HET K A 803 1 HET K A 804 1 HET RED B 801 9 HET ZN B 802 1 HET K B 803 1 HET K B 804 1 HETNAM RED DIHYDROLIPOIC ACID HETNAM ZN ZINC ION HETNAM K POTASSIUM ION FORMUL 3 RED 2(C8 H16 O2 S2) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 K 4(K 1+) FORMUL 11 HOH *132(H2 O) HELIX 1 AA1 ASP A 449 HIS A 455 5 7 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 GLU A 528 1 11 HELIX 8 AA8 GLU A 537 THR A 558 1 22 HELIX 9 AA9 ASN A 587 ILE A 599 1 13 HELIX 10 AB1 GLY A 616 PHE A 623 1 8 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 ASP B 449 HIS B 455 5 7 HELIX 21 AC3 PRO B 467 LEU B 480 1 14 HELIX 22 AC4 LEU B 482 CYS B 486 5 5 HELIX 23 AC5 THR B 495 ALA B 500 1 6 HELIX 24 AC6 SER B 504 SER B 514 1 11 HELIX 25 AC7 GLU B 515 MET B 517 5 3 HELIX 26 AC8 LYS B 518 GLU B 528 1 11 HELIX 27 AC9 GLU B 537 THR B 558 1 22 HELIX 28 AD1 ASN B 587 ILE B 599 1 13 HELIX 29 AD2 GLY B 616 PHE B 623 1 8 HELIX 30 AD3 GLU B 638 ALA B 641 5 4 HELIX 31 AD4 SER B 646 ASN B 650 5 5 HELIX 32 AD5 LEU B 656 ARG B 660 5 5 HELIX 33 AD6 GLY B 674 LEU B 685 1 12 HELIX 34 AD7 LEU B 685 ALA B 694 1 10 HELIX 35 AD8 THR B 718 MET B 730 1 13 HELIX 36 AD9 SER B 731 GLY B 735 5 5 HELIX 37 AE1 ASN B 746 LEU B 762 1 17 HELIX 38 AE2 LYS B 776 ALA B 791 1 16 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 ILE A 740 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 LEU A 630 N ILE A 608 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O VAL A 664 N TYR A 631 SHEET 1 AA2 8 HIS B 487 ARG B 488 0 SHEET 2 AA2 8 THR B 444 VAL B 447 1 N THR B 444 O HIS B 487 SHEET 3 AA2 8 ASN B 563 ALA B 566 1 O ASN B 563 N GLY B 445 SHEET 4 AA2 8 VAL B 737 LEU B 741 1 O ILE B 739 N ALA B 566 SHEET 5 AA2 8 LEU B 697 ALA B 702 1 N VAL B 700 O ILE B 740 SHEET 6 AA2 8 VAL B 606 ASP B 610 1 N LEU B 607 O LEU B 699 SHEET 7 AA2 8 VAL B 629 ARG B 636 1 O LEU B 630 N ILE B 608 SHEET 8 AA2 8 ASN B 663 TRP B 668 1 O VAL B 664 N TYR B 631 LINK O ASP A 610 K K A 804 1555 1555 2.82 LINK OD1 ASP A 610 K K A 804 1555 1555 2.99 LINK OD1 ASP A 612 ZN ZN A 802 1555 1555 2.09 LINK O ASP A 612 K K A 804 1555 1555 2.51 LINK ND1 HIS A 614 ZN ZN A 802 1555 1555 2.30 LINK O HIS A 614 K K A 804 1555 1555 2.84 LINK O PHE A 623 K K A 803 1555 1555 2.57 LINK O ASP A 626 K K A 803 1555 1555 2.90 LINK O VAL A 629 K K A 803 1555 1555 2.79 LINK OG SER A 633 K K A 804 1555 1555 2.73 LINK O LEU A 634 K K A 804 1555 1555 2.70 LINK O TYR A 662 K K A 803 1555 1555 2.71 LINK OD2 ASP A 705 ZN ZN A 802 1555 1555 1.91 LINK S8 RED A 801 ZN ZN A 802 1555 1555 2.30 LINK K K A 803 O HOH A 914 1555 1555 2.62 LINK K K A 803 O HOH A 936 1555 1555 3.07 LINK O ASP B 610 K K B 804 1555 1555 2.86 LINK OD1 ASP B 610 K K B 804 1555 1555 2.83 LINK OD1 ASP B 612 ZN ZN B 802 1555 1555 2.00 LINK O ASP B 612 K K B 804 1555 1555 2.55 LINK ND1 HIS B 614 ZN ZN B 802 1555 1555 2.30 LINK O HIS B 614 K K B 804 1555 1555 2.88 LINK O PHE B 623 K K B 803 1555 1555 2.49 LINK O ASP B 626 K K B 803 1555 1555 2.91 LINK O VAL B 629 K K B 803 1555 1555 2.74 LINK OG SER B 633 K K B 804 1555 1555 2.85 LINK O LEU B 634 K K B 804 1555 1555 2.81 LINK O TYR B 662 K K B 803 1555 1555 2.93 LINK OD2 ASP B 705 ZN ZN B 802 1555 1555 1.95 LINK S8 RED B 801 ZN ZN B 802 1555 1555 2.36 LINK K K B 803 O HOH B 917 1555 1555 2.72 LINK K K B 803 O HOH B 929 1555 1555 2.98 CISPEP 1 ARG A 569 PRO A 570 0 -1.24 CISPEP 2 PHE A 643 PRO A 644 0 6.92 CISPEP 3 ARG B 569 PRO B 570 0 -1.00 CISPEP 4 PHE B 643 PRO B 644 0 6.81 CRYST1 74.894 92.156 96.666 90.00 90.00 90.00 P 21 21 21 8 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 0.013352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010345 0.00000 MTRIX1 1 -0.999923 -0.009621 -0.007816 74.87794 1 MTRIX2 1 -0.009731 0.999854 0.014062 0.22820 1 MTRIX3 1 0.007680 0.014137 -0.999871 22.17040 1