HEADER METAL BINDING PROTEIN 07-DEC-17 5YY0 TITLE CRYSTAL STRUCTURE OF THE HYHL-HYPA COMPLEX (FORM II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSOLIC NIFE-HYDROGENASE, ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SULFHYDROGENASE ALPHA SUBUNIT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROBABLE HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 SOURCE 3 / JCM 12380 / KOD1); SOURCE 4 ORGANISM_COMMON: PYROCOCCUS KODAKARAENSIS (STRAIN KOD1); SOURCE 5 ORGANISM_TAXID: 69014; SOURCE 6 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 7 GENE: HYDA, TK2069; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 SOURCE 13 / JCM 12380 / KOD1); SOURCE 14 ORGANISM_COMMON: PYROCOCCUS KODAKARAENSIS (STRAIN KOD1); SOURCE 15 ORGANISM_TAXID: 69014; SOURCE 16 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 17 GENE: HYPA, TK2008; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROGENASE, MATURATION, HYHL, HYPA, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KWON,S.WATANABE,Y.NISHITANI,K.MIKI REVDAT 3 27-MAR-24 5YY0 1 REMARK REVDAT 2 18-JUL-18 5YY0 1 JRNL REVDAT 1 20-JUN-18 5YY0 0 JRNL AUTH S.KWON,S.WATANABE,Y.NISHITANI,T.KAWASHIMA,T.KANAI,H.ATOMI, JRNL AUTH 2 K.MIKI JRNL TITL CRYSTAL STRUCTURES OF A [NIFE] HYDROGENASE LARGE SUBUNIT JRNL TITL 2 HYHL IN AN IMMATURE STATE IN COMPLEX WITH A NI CHAPERONE JRNL TITL 3 HYPA. JRNL REF PROC. NATL. ACAD. SCI. V. 115 7045 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29915046 JRNL DOI 10.1073/PNAS.1801955115 REMARK 2 REMARK 2 RESOLUTION. 3.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.292 REMARK 3 R VALUE (WORKING SET) : 0.290 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 625 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 44.0194 - 5.1457 0.95 3050 161 0.2488 0.2557 REMARK 3 2 5.1457 - 4.0852 0.95 2940 154 0.3159 0.3600 REMARK 3 3 4.0852 - 3.5691 0.95 2919 145 0.3596 0.3746 REMARK 3 4 3.5691 - 3.2429 0.95 2917 165 0.3666 0.4370 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 47.360 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 : 0.003 3782 REMARK 3 ANGLE : 0.793 5158 REMARK 3 CHIRALITY : 0.032 618 REMARK 3 PLANARITY : 0.004 676 REMARK 3 DIHEDRAL : 9.952 1264 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 5YY0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12459 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.243 REMARK 200 RESOLUTION RANGE LOW (A) : 44.015 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.20 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.62200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 58.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NACL, 0.1M MGCL2, 12% PEG 3350, REMARK 280 0.1M IMIDAZOLE-HCL (PH 6.2), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 15 REMARK 465 VAL A 16 REMARK 465 GLU A 17 REMARK 465 GLY A 18 REMARK 465 LYS A 19 REMARK 465 SER A 156 REMARK 465 ARG A 157 REMARK 465 ALA A 158 REMARK 465 ILE A 159 REMARK 465 GLU A 207 REMARK 465 VAL A 208 REMARK 465 GLU A 209 REMARK 465 GLY A 210 REMARK 465 PRO A 211 REMARK 465 ILE A 212 REMARK 465 HIS A 396 REMARK 465 TYR A 397 REMARK 465 ASN A 398 REMARK 465 ASP A 399 REMARK 465 ASP A 400 REMARK 465 PRO A 401 REMARK 465 GLU A 402 REMARK 465 ARG A 427 REMARK 465 LEU A 428 REMARK 465 MET B 1 REMARK 465 PHE B 89 REMARK 465 ASP B 90 REMARK 465 GLU B 91 REMARK 465 ARG B 92 REMARK 465 ILE B 93 REMARK 465 LYS B 94 REMARK 465 GLU B 95 REMARK 465 ASP B 96 REMARK 465 GLU B 136 REMARK 465 GLY B 137 REMARK 465 GLY B 138 REMARK 465 SER B 139 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 TYR A 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 6 CG CD1 CD2 REMARK 470 ASP A 11 CG OD1 OD2 REMARK 470 HIS A 12 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 13 CG1 CG2 CD1 REMARK 470 ILE A 24 CG1 CG2 CD1 REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 ASN A 37 CG OD1 ND2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 67 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 LEU A 95 CG CD1 CD2 REMARK 470 LEU A 110 CG CD1 CD2 REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 LEU A 141 CG CD1 CD2 REMARK 470 ASP A 152 CG OD1 OD2 REMARK 470 HIS A 160 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 171 CG CD CE NZ REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 ARG A 183 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 GLU A 193 CG CD OE1 OE2 REMARK 470 THR A 200 OG1 CG2 REMARK 470 TYR A 205 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 206 CG CD OE1 OE2 REMARK 470 HIS A 214 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 224 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 227 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 229 CG OD1 OD2 REMARK 470 TYR A 230 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 SER A 234 OG REMARK 470 ASP A 235 CG OD1 OD2 REMARK 470 ASN A 237 CG OD1 ND2 REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 TYR A 244 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A 247 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 250 CG CD OE1 OE2 REMARK 470 PHE A 251 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 252 CG1 CG2 REMARK 470 PHE A 257 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 TYR A 263 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 266 CG CD CE NZ REMARK 470 TYR A 284 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 288 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 GLU A 292 CG CD OE1 OE2 REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 ASP A 296 CG OD1 OD2 REMARK 470 LYS A 331 CG CD CE NZ REMARK 470 TRP A 332 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 332 CZ3 CH2 REMARK 470 ILE A 334 CG1 CG2 CD1 REMARK 470 ARG A 335 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 337 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 470 VAL A 340 CG1 CG2 REMARK 470 LEU A 342 CG CD1 CD2 REMARK 470 ASP A 344 CG OD1 OD2 REMARK 470 VAL A 348 CG1 CG2 REMARK 470 ARG A 368 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 382 CG CD1 CD2 REMARK 470 GLN A 387 CG CD OE1 NE2 REMARK 470 LYS A 395 CG CD CE NZ REMARK 470 LYS A 403 CG CD CE NZ REMARK 470 LEU A 404 CG CD1 CD2 REMARK 470 LYS A 405 CG CD CE NZ REMARK 470 TYR A 415 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 420 OG REMARK 470 HIS A 424 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 425 CG1 CG2 REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 19 CG CD OE1 NE2 REMARK 470 ARG B 25 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 ASN B 75 CG OD1 ND2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 VAL B 85 CG1 CG2 REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 ILE B 97 CG1 CG2 CD1 REMARK 470 HIS B 98 CG ND1 CD2 CE1 NE2 REMARK 470 PHE B 99 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B 100 CG1 CG2 CD1 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 VAL B 104 CG1 CG2 REMARK 470 PHE B 107 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 PHE B 118 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 119 CG CD OE1 OE2 REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 LYS B 135 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 O TYR A 113 OH TYR A 133 1.80 REMARK 500 OH TYR A 113 OG1 THR A 195 1.87 REMARK 500 CG HIS A 111 OD1 ASP A 416 1.94 REMARK 500 CA ALA B 109 CD2 HIS B 116 2.06 REMARK 500 CB ALA B 109 NE2 HIS B 116 2.15 REMARK 500 OH TYR A 100 O GLU A 352 2.17 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 OH TYR A 194 O HIS B 98 4567 2.05 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 PRO A 62 4.12 -69.08 REMARK 500 CYS B 76 10.96 -149.26 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 ZN B 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 73 SG REMARK 620 2 CYS B 76 SG 127.5 REMARK 620 3 CYS B 110 SG 98.3 128.8 REMARK 620 4 CYS B 113 SG 83.1 112.9 92.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 701 DBREF 5YY0 A 1 428 UNP Q8NKS2 Q8NKS2_THEKO 1 428 DBREF 5YY0 B 1 139 UNP Q5JIH3 HYPA_THEKO 1 139 SEQRES 1 A 428 MET LYS ASN VAL TYR LEU PRO ILE THR VAL ASP HIS ILE SEQRES 2 A 428 ALA ARG VAL GLU GLY LYS GLY GLY VAL GLU ILE VAL VAL SEQRES 3 A 428 GLY ASP ASP GLY VAL LYS GLU VAL LYS LEU ASN ILE ILE SEQRES 4 A 428 GLU GLY PRO ARG PHE PHE GLU ALA ILE THR LEU GLY LYS SEQRES 5 A 428 LYS LEU ASP GLU ALA LEU ALA ILE TYR PRO ARG ILE CYS SEQRES 6 A 428 SER PHE CYS SER ALA ALA HIS LYS LEU THR ALA VAL GLU SEQRES 7 A 428 ALA ALA GLU LYS ALA ILE GLY PHE THR PRO ARG GLU GLU SEQRES 8 A 428 ILE GLN ALA LEU ARG GLU VAL LEU TYR ILE GLY ASP MET SEQRES 9 A 428 ILE GLU SER HIS ALA LEU HIS LEU TYR LEU LEU VAL LEU SEQRES 10 A 428 PRO ASP TYR LEU GLY TYR SER GLY PRO LEU HIS MET ILE SEQRES 11 A 428 ASP GLU TYR LYS LYS GLU MET SER ILE ALA LEU ASP LEU SEQRES 12 A 428 LYS ASN LEU GLY SER TRP MET MET ASP GLU LEU GLY SER SEQRES 13 A 428 ARG ALA ILE HIS GLN GLU ASN ALA VAL LEU GLY GLY PHE SEQRES 14 A 428 GLY LYS LEU PRO ASP LYS SER VAL LEU GLU ASN MET LYS SEQRES 15 A 428 ARG ARG LEU LYS GLU ALA LEU PRO LYS ALA GLU TYR THR SEQRES 16 A 428 PHE GLU LEU PHE THR LYS LEU GLU GLN TYR GLU GLU VAL SEQRES 17 A 428 GLU GLY PRO ILE THR HIS ILE ALA VAL LYS PRO ARG ASN SEQRES 18 A 428 GLY VAL TYR GLY ILE TYR GLY ASP TYR LEU LYS ALA SER SEQRES 19 A 428 ASP GLY ASN GLU PHE PRO SER GLU GLU TYR ARG GLU HIS SEQRES 20 A 428 ILE LYS GLU PHE VAL VAL GLU HIS SER PHE ALA LYS HIS SEQRES 21 A 428 SER HIS TYR HIS GLY LYS PRO PHE MET VAL GLY ALA ILE SEQRES 22 A 428 SER ARG LEU VAL ASN ASN ALA ASP THR LEU TYR GLY ARG SEQRES 23 A 428 ALA LYS GLU LEU TYR GLU SER TYR LYS ASP LEU LEU ARG SEQRES 24 A 428 SER THR ASN PRO PHE ALA ASN ASN LEU ALA GLN ALA LEU SEQRES 25 A 428 GLU LEU VAL TYR PHE THR GLU ARG ALA ILE ASP LEU ILE SEQRES 26 A 428 ASP GLU ALA LEU ALA LYS TRP PRO ILE ARG PRO ARG ASP SEQRES 27 A 428 GLU VAL ALA LEU LYS ASP GLY PHE GLY VAL SER THR THR SEQRES 28 A 428 GLU ALA PRO ARG GLY VAL LEU VAL TYR ALA LEU LYS VAL SEQRES 29 A 428 GLU ASN GLY ARG VAL SER TYR ALA ASP ILE ILE THR PRO SEQRES 30 A 428 THR ALA PHE ASN LEU ALA MET MET GLU GLN HIS VAL ARG SEQRES 31 A 428 MET MET ALA GLU LYS HIS TYR ASN ASP ASP PRO GLU LYS SEQRES 32 A 428 LEU LYS LEU LEU ALA GLU MET VAL VAL ARG ALA TYR ASP SEQRES 33 A 428 PRO CYS ILE SER CYS SER VAL HIS VAL ALA ARG LEU SEQRES 1 B 139 MET HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 B 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 B 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 B 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 B 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 B 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 B 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 B 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 B 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 B 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 B 139 ILE LYS ILE GLU LYS GLU GLY GLY SER HET ZN B 701 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 PRO A 42 THR A 49 1 8 HELIX 2 AA2 LYS A 53 TYR A 61 1 9 HELIX 3 AA3 PRO A 62 ILE A 64 5 3 HELIX 4 AA4 CYS A 65 PHE A 67 5 3 HELIX 5 AA5 CYS A 68 GLY A 85 1 18 HELIX 6 AA6 ARG A 89 GLY A 122 1 34 HELIX 7 AA7 TYR A 133 GLY A 155 1 23 HELIX 8 AA8 ASP A 174 LEU A 202 1 29 HELIX 9 AA9 VAL A 252 SER A 256 5 5 HELIX 10 AB1 TYR A 263 LYS A 266 5 4 HELIX 11 AB2 GLY A 271 ASN A 279 1 9 HELIX 12 AB3 GLY A 285 TYR A 294 1 10 HELIX 13 AB4 PHE A 304 LEU A 329 1 26 HELIX 14 AB5 THR A 376 HIS A 388 1 13 HELIX 15 AB6 LEU A 404 ALA A 414 1 11 HELIX 16 AB7 GLU B 3 GLY B 22 1 20 HELIX 17 AB8 ALA B 40 PHE B 52 1 13 HELIX 18 AB9 LEU B 82 ASP B 87 1 6 HELIX 19 AC1 VAL B 103 LEU B 108 1 6 SHEET 1 AA1 4 PRO A 7 HIS A 12 0 SHEET 2 AA1 4 VAL B 126 GLU B 134 -1 O ALA B 129 N ILE A 8 SHEET 3 AA1 4 ARG B 25 GLY B 34 -1 N ARG B 30 O GLY B 130 SHEET 4 AA1 4 GLU B 61 GLU B 67 1 O GLU B 67 N LEU B 33 SHEET 1 AA2 3 GLU A 33 LEU A 36 0 SHEET 2 AA2 3 VAL A 22 VAL A 25 -1 N GLU A 23 O LYS A 35 SHEET 3 AA2 3 SER A 422 VAL A 425 1 O VAL A 423 N ILE A 24 SHEET 1 AA3 4 LEU A 231 LYS A 232 0 SHEET 2 AA3 4 GLY A 345 ALA A 353 -1 O THR A 350 N LYS A 232 SHEET 3 AA3 4 GLY A 356 GLU A 365 -1 O VAL A 364 N GLY A 345 SHEET 4 AA3 4 ARG A 368 ILE A 375 -1 O ILE A 375 N VAL A 359 SHEET 1 AA4 2 ILE A 248 GLU A 250 0 SHEET 2 AA4 2 LYS A 259 SER A 261 -1 O HIS A 260 N LYS A 249 SHEET 1 AA5 3 TYR B 78 LYS B 81 0 SHEET 2 AA5 3 VAL B 70 CYS B 73 -1 N PHE B 71 O TRP B 80 SHEET 3 AA5 3 PHE B 118 LYS B 122 -1 O GLU B 119 N LYS B 72 LINK SG CYS B 73 ZN ZN B 701 1555 1555 2.61 LINK SG CYS B 76 ZN ZN B 701 1555 1555 2.02 LINK SG CYS B 110 ZN ZN B 701 1555 1555 2.11 LINK SG CYS B 113 ZN ZN B 701 1555 1555 2.62 SITE 1 AC1 4 CYS B 73 CYS B 76 CYS B 110 CYS B 113 CRYST1 132.046 132.046 132.046 90.00 90.00 90.00 P 2 3 12 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 0.007573 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007573 0.00000