HEADER METAL BINDING PROTEIN/HYDROLASE 27-MAY-15 5AUN TITLE CRYSTAL STRUCTURE OF THE HYPAB-NI COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ATPASE INVOLVED IN CHROMOSOME PARTITIONING, PARA/MIND COMPND 7 FAMILY, MRP HOMOLOG; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HYPB; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARAENSIS (STRAIN ATCC BAA-918 SOURCE 3 / JCM 12380 / KOD1); SOURCE 4 ORGANISM_TAXID: 69014; SOURCE 5 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 6 GENE: HYPA, TK2008; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARAENSIS (STRAIN ATCC BAA-918 SOURCE 12 / JCM 12380 / KOD1); SOURCE 13 ORGANISM_TAXID: 69014; SOURCE 14 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 15 GENE: TK2007; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN COMPLEX, METALLOCHAPERONE, METAL BINDING PROTEIN-HYDROLASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,T.KAWASHIMA,Y.NISHITANI,K.MIKI REVDAT 4 08-NOV-23 5AUN 1 LINK REVDAT 3 19-FEB-20 5AUN 1 SOURCE KEYWDS JRNL REMARK REVDAT 2 08-JUL-15 5AUN 1 JRNL REVDAT 1 24-JUN-15 5AUN 0 JRNL AUTH S.WATANABE,T.KAWASHIMA,Y.NISHITANI,T.KANAI,T.WADA,K.INABA, JRNL AUTH 2 H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL STRUCTURAL BASIS OF A NI ACQUISITION CYCLE FOR [NIFE] JRNL TITL 2 HYDROGENASE BY NI-METALLOCHAPERONE HYPA AND ITS ENHANCER JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 7701 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26056269 JRNL DOI 10.1073/PNAS.1503102112 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 96888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 4910 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 37.3698 - 5.0603 1.00 3106 147 0.1754 0.2345 REMARK 3 2 5.0603 - 4.0180 1.00 3086 164 0.1344 0.1390 REMARK 3 3 4.0180 - 3.5105 1.00 3066 172 0.1433 0.1667 REMARK 3 4 3.5105 - 3.1897 1.00 3100 149 0.1611 0.1726 REMARK 3 5 3.1897 - 2.9612 1.00 3094 153 0.1757 0.2156 REMARK 3 6 2.9612 - 2.7867 1.00 3103 150 0.1815 0.1965 REMARK 3 7 2.7867 - 2.6472 1.00 3068 172 0.1776 0.2419 REMARK 3 8 2.6472 - 2.5320 1.00 3051 194 0.1768 0.1933 REMARK 3 9 2.5320 - 2.4345 1.00 3090 148 0.1741 0.1978 REMARK 3 10 2.4345 - 2.3505 1.00 3104 151 0.1742 0.1829 REMARK 3 11 2.3505 - 2.2770 1.00 3077 174 0.1737 0.2063 REMARK 3 12 2.2770 - 2.2120 1.00 3088 172 0.1833 0.2210 REMARK 3 13 2.2120 - 2.1537 1.00 3067 159 0.1821 0.2555 REMARK 3 14 2.1537 - 2.1012 1.00 3076 161 0.1885 0.2427 REMARK 3 15 2.1012 - 2.0534 1.00 3096 174 0.1948 0.2403 REMARK 3 16 2.0534 - 2.0097 1.00 3068 155 0.1893 0.2259 REMARK 3 17 2.0097 - 1.9695 1.00 3106 156 0.1939 0.2339 REMARK 3 18 1.9695 - 1.9324 1.00 3088 173 0.1989 0.2328 REMARK 3 19 1.9324 - 1.8979 1.00 3059 173 0.2095 0.2809 REMARK 3 20 1.8979 - 1.8657 1.00 3036 177 0.2196 0.2210 REMARK 3 21 1.8657 - 1.8356 1.00 3118 146 0.2388 0.2773 REMARK 3 22 1.8356 - 1.8073 1.00 3096 164 0.2420 0.3386 REMARK 3 23 1.8073 - 1.7808 1.00 3095 181 0.2552 0.2728 REMARK 3 24 1.7808 - 1.7557 1.00 3047 158 0.2629 0.3286 REMARK 3 25 1.7557 - 1.7320 1.00 3092 157 0.2656 0.2959 REMARK 3 26 1.7320 - 1.7095 1.00 3062 172 0.2649 0.3049 REMARK 3 27 1.7095 - 1.6881 1.00 3118 155 0.2878 0.3218 REMARK 3 28 1.6881 - 1.6678 0.99 3045 172 0.2976 0.3467 REMARK 3 29 1.6678 - 1.6484 0.98 2994 177 0.3148 0.3201 REMARK 3 30 1.6484 - 1.6298 0.88 2682 154 0.3056 0.3426 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.86 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 3105 REMARK 3 ANGLE : 0.907 4184 REMARK 3 CHIRALITY : 0.034 477 REMARK 3 PLANARITY : 0.004 539 REMARK 3 DIHEDRAL : 14.312 1147 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: THE STRUCTURAL FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5AUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1300000009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.95700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3A43 AND 3VX3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, PEG3350, PH 6.2, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 37.36000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.37200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.36000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.37200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 537 LIES ON A SPECIAL POSITION. 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 GLY A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 ARG B 191 REMARK 465 SER B 192 REMARK 465 GLU B 193 REMARK 465 GLN B 194 REMARK 465 LEU B 195 REMARK 465 ASP B 196 REMARK 465 ASP B 197 REMARK 465 GLU B 198 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 LYS A 83 CG CD CE NZ REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 GLU B 73 CG CD OE1 OE2 REMARK 470 LYS B 199 CG CD CE NZ REMARK 470 LYS B 203 CG CD CE NZ REMARK 470 GLU B 206 CG CD OE1 OE2 REMARK 470 GLU B 230 CG CD OE1 OE2 REMARK 470 GLU B 231 CG CD OE1 OE2 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 HOH B 600 O HOH B 604 1.84 REMARK 500 O LYS A 88 O HOH A 301 1.95 REMARK 500 O HOH A 303 O HOH A 410 2.00 REMARK 500 OE2 GLU B 236 O HOH B 401 2.02 REMARK 500 OD1 ASP B 221 O HOH B 402 2.11 REMARK 500 OE1 GLU A 49 O HOH A 302 2.11 REMARK 500 OE1 GLU A 68 O HOH A 303 2.15 REMARK 500 OE2 GLU A 79 O HOH A 304 2.16 REMARK 500 O HOH B 492 O HOH B 550 2.17 REMARK 500 O HOH B 405 O HOH B 600 2.19 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 O HOH A 444 O HOH B 584 2554 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER B 26 -24.91 -157.25 REMARK 500 ASP B 78 86.77 -161.75 REMARK 500 ASP B 78 85.68 -161.75 REMARK 500 ASP B 124 -132.89 53.92 REMARK 500 LEU B 148 71.10 -116.93 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 NI A 202 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 MET A 1 N 2.9 REMARK 620 3 HIS A 2 N 84.9 83.6 REMARK 620 4 HIS A 2 ND1 173.9 174.6 91.6 REMARK 620 5 HIS A 98 NE2 91.8 93.1 175.5 91.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 73 SG REMARK 620 2 CYS A 76 SG 114.8 REMARK 620 3 CYS A 110 SG 107.1 105.4 REMARK 620 4 CYS A 113 SG 100.7 116.9 111.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 310 O REMARK 620 2 HOH A 323 O 82.3 REMARK 620 3 LYS B 149 O 96.7 92.1 REMARK 620 4 HOH B 416 O 93.5 175.7 88.7 REMARK 620 5 HOH B 473 O 91.9 87.9 171.3 92.0 REMARK 620 6 HOH B 550 O 172.0 100.7 90.7 83.5 80.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 34 OG REMARK 620 2 ADP B 301 O1B 92.1 REMARK 620 3 HOH B 421 O 87.9 83.0 REMARK 620 4 HOH B 422 O 87.9 170.7 87.7 REMARK 620 5 HOH B 423 O 81.7 95.3 169.5 93.8 REMARK 620 6 HOH B 519 O 170.0 95.8 99.0 85.3 91.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue URE A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue URE A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue URE A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A43 RELATED DB: PDB REMARK 900 3A43 IS AN ISOLATED STRUCTURE OF THE SAME PROTEIN REMARK 900 RELATED ID: 3VX3 RELATED DB: PDB REMARK 900 3VX3 IS AN ISOLATED STRUCTURE OF THE SAME PROTEIN REMARK 900 RELATED ID: 5AUO RELATED DB: PDB REMARK 900 RELATED ID: 5AUP RELATED DB: PDB REMARK 900 RELATED ID: 5AUQ RELATED DB: PDB DBREF 5AUN A 1 139 UNP Q5JIH3 HYPA_THEKO 1 139 DBREF 5AUN B 1 248 UNP Q5JIH4 Q5JIH4_THEKO 1 248 SEQRES 1 A 139 MET HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 A 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 A 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 A 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 A 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 A 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 A 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 A 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 A 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 A 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 A 139 ILE LYS ILE GLU LYS GLU GLY GLY SER SEQRES 1 B 248 MET ASN ALA ILE ASP PRO ARG GLU ILE ALA ILE ASN ALA SEQRES 2 B 248 ARG LEU GLU GLY VAL LYS ARG ILE ILE PRO VAL VAL SER SEQRES 3 B 248 GLY LYS GLY GLY VAL GLY LYS SER LEU VAL SER THR THR SEQRES 4 B 248 LEU ALA LEU VAL LEU ALA GLU LYS GLY TYR ARG VAL GLY SEQRES 5 B 248 LEU LEU ASP LEU ASP PHE HIS GLY ALA SER ASP HIS VAL SEQRES 6 B 248 ILE LEU GLY PHE GLU PRO LYS GLU PHE PRO GLU GLU ASP SEQRES 7 B 248 ARG GLY VAL VAL PRO PRO THR VAL HIS GLY ILE LYS PHE SEQRES 8 B 248 MET THR ILE ALA TYR TYR THR GLU ASP ARG PRO THR PRO SEQRES 9 B 248 LEU ARG GLY LYS GLU ILE SER ASP ALA LEU ILE GLU LEU SEQRES 10 B 248 LEU THR ILE THR ARG TRP ASP GLU LEU ASP TYR LEU VAL SEQRES 11 B 248 ILE ASP MET PRO PRO GLY LEU GLY ASP GLN LEU LEU ASP SEQRES 12 B 248 VAL LEU ARG PHE LEU LYS ARG GLY GLU PHE LEU VAL VAL SEQRES 13 B 248 ALA THR PRO SER LYS LEU SER LEU ASN VAL VAL ARG LYS SEQRES 14 B 248 LEU ILE GLU LEU LEU LYS GLU GLU GLY HIS LYS VAL ILE SEQRES 15 B 248 GLY VAL VAL GLU ASN MET LYS LEU ARG SER GLU GLN LEU SEQRES 16 B 248 ASP ASP GLU LYS ASP VAL GLU LYS LEU ALA GLU GLU PHE SEQRES 17 B 248 GLY VAL PRO TYR LEU VAL GLY ILE PRO PHE TYR PRO ASP SEQRES 18 B 248 LEU ASP ALA LYS VAL GLY ASN VAL GLU GLU LEU MET LYS SEQRES 19 B 248 THR GLU PHE ALA GLY LYS VAL ARG GLU LEU ALA GLY ARG SEQRES 20 B 248 LEU HET ZN A 201 1 HET NI A 202 1 HET URE A 203 4 HET URE A 204 4 HET URE A 205 4 HET CL A 206 1 HET GOL A 207 6 HET ADP B 301 27 HET MG B 302 1 HET MG B 303 1 HET GOL B 304 6 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM URE UREA HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN ZN 2+ FORMUL 4 NI NI 2+ FORMUL 5 URE 3(C H4 N2 O) FORMUL 8 CL CL 1- FORMUL 9 GOL 2(C3 H8 O3) FORMUL 10 ADP C10 H15 N5 O10 P2 FORMUL 11 MG 2(MG 2+) FORMUL 14 HOH *349(H2 O) HELIX 1 AA1 HIS A 2 GLU A 21 1 20 HELIX 2 AA2 LEU A 36 ASP A 38 5 3 HELIX 3 AA3 ALA A 40 ALA A 53 1 14 HELIX 4 AA4 LYS A 83 PHE A 89 5 7 HELIX 5 AA5 ASP A 90 ILE A 100 1 11 HELIX 6 AA6 VAL A 103 LEU A 108 1 6 HELIX 7 AA7 ILE B 9 LEU B 15 1 7 HELIX 8 AA8 GLY B 32 LYS B 47 1 16 HELIX 9 AA9 SER B 62 GLY B 68 1 7 HELIX 10 AB1 ALA B 95 THR B 98 5 4 HELIX 11 AB2 ARG B 106 THR B 121 1 16 HELIX 12 AB3 GLY B 138 LEU B 148 1 11 HELIX 13 AB4 SER B 160 GLU B 177 1 18 HELIX 14 AB5 ASP B 200 PHE B 208 1 9 HELIX 15 AB6 ASP B 221 LYS B 225 5 5 HELIX 16 AB7 ASN B 228 MET B 233 1 6 HELIX 17 AB8 THR B 235 GLY B 246 1 12 SHEET 1 AA1 3 GLU A 61 GLU A 67 0 SHEET 2 AA1 3 ARG A 25 GLY A 34 1 N VAL A 31 O GLU A 63 SHEET 3 AA1 3 VAL A 126 GLU A 134 -1 O TYR A 127 N VAL A 32 SHEET 1 AA2 3 GLU A 79 LYS A 81 0 SHEET 2 AA2 3 VAL A 70 CYS A 73 -1 N PHE A 71 O TRP A 80 SHEET 3 AA2 3 PHE A 118 LYS A 122 -1 O GLU A 119 N LYS A 72 SHEET 1 AA3 8 THR B 85 VAL B 86 0 SHEET 2 AA3 8 ILE B 89 THR B 93 -1 O ILE B 89 N VAL B 86 SHEET 3 AA3 8 VAL B 51 ASP B 55 1 N LEU B 53 O LYS B 90 SHEET 4 AA3 8 LEU B 126 ASP B 132 1 O VAL B 130 N GLY B 52 SHEET 5 AA3 8 VAL B 18 VAL B 25 1 N VAL B 24 O ILE B 131 SHEET 6 AA3 8 GLU B 152 ALA B 157 1 O VAL B 156 N VAL B 25 SHEET 7 AA3 8 LYS B 180 LYS B 189 1 O VAL B 185 N VAL B 155 SHEET 8 AA3 8 TYR B 212 PRO B 217 1 O ILE B 216 N GLU B 186 LINK N AMET A 1 NI NI A 202 1555 1555 1.98 LINK N BMET A 1 NI NI A 202 1555 1555 2.10 LINK N HIS A 2 NI NI A 202 1555 1555 1.96 LINK ND1 HIS A 2 NI NI A 202 1555 1555 2.02 LINK SG CYS A 73 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 76 ZN ZN A 201 1555 1555 2.31 LINK NE2 HIS A 98 NI NI A 202 1555 1555 1.94 LINK SG CYS A 110 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 113 ZN ZN A 201 1555 1555 2.33 LINK O HOH A 310 MG MG B 303 3555 1555 2.12 LINK O HOH A 323 MG MG B 303 3555 1555 2.22 LINK OG SER B 34 MG MG B 302 1555 1555 2.13 LINK O LYS B 149 MG MG B 303 1555 1555 2.10 LINK O1B ADP B 301 MG MG B 302 1555 1555 2.08 LINK MG MG B 302 O HOH B 421 1555 1555 2.18 LINK MG MG B 302 O HOH B 422 1555 1555 2.07 LINK MG MG B 302 O HOH B 423 1555 1555 2.11 LINK MG MG B 302 O HOH B 519 1555 1555 2.12 LINK MG MG B 303 O HOH B 416 1555 1555 2.13 LINK MG MG B 303 O HOH B 473 1555 1555 2.11 LINK MG MG B 303 O HOH B 550 1555 1555 2.28 SITE 1 AC1 4 CYS A 73 CYS A 76 CYS A 110 CYS A 113 SITE 1 AC2 4 MET A 1 HIS A 2 GLU A 3 HIS A 98 SITE 1 AC3 4 GLU A 35 LEU A 36 ASP A 38 LYS A 94 SITE 1 AC4 4 GLU A 41 PHE A 64 HOH A 356 HOH A 387 SITE 1 AC5 5 ILE A 131 LYS A 132 HOH A 380 LYS B 234 SITE 2 AC5 5 GLU B 236 SITE 1 AC6 4 GLN A 19 THR A 55 ILE A 56 HOH A 429 SITE 1 AC7 1 ASP B 5 SITE 1 AC8 24 LYS B 28 GLY B 30 VAL B 31 GLY B 32 SITE 2 AC8 24 LYS B 33 SER B 34 LEU B 35 SER B 160 SITE 3 AC8 24 LEU B 162 ASN B 187 MET B 188 PRO B 217 SITE 4 AC8 24 PHE B 218 TYR B 219 LEU B 222 PHE B 237 SITE 5 AC8 24 MG B 302 HOH B 411 HOH B 412 HOH B 421 SITE 6 AC8 24 HOH B 423 HOH B 489 HOH B 519 HOH B 538 SITE 1 AC9 6 SER B 34 ADP B 301 HOH B 421 HOH B 422 SITE 2 AC9 6 HOH B 423 HOH B 519 SITE 1 AD1 6 HOH A 310 HOH A 323 LYS B 149 HOH B 416 SITE 2 AD1 6 HOH B 473 HOH B 550 SITE 1 AD2 4 TRP A 4 TYR A 78 ARG B 79 HOH B 420 CRYST1 74.720 82.744 65.128 90.00 90.00 90.00 P 21 21 2 4 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 0.013383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015354 0.00000