HEADER LIGASE 15-OCT-24 9K04 TITLE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI AIR SYNTHETASE H239A MUTANT TITLE 2 BOUND TO ADP AND PI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AIR SYNTHASE,AIRS,PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE; COMPND 5 EC: 6.3.3.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI GE5; SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 GENE: PURM, PYRAB16520, PAB1083; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PURINE SYNTHESIS, ATP HYDROLYSIS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.CHEN,C.J.CHEN REVDAT 2 11-FEB-26 9K04 1 JRNL REVDAT 1 15-OCT-25 9K04 0 JRNL AUTH Y.H.CHEN,Y.C.HUANG,R.G.R.RAO,H.C.CHANG,Y.H.LAN,A.NAKAGAWA, JRNL AUTH 2 J.JEYARAMAN,C.J.CHEN JRNL TITL STRUCTURAL INSIGHTS INTO SUBSTRATE BINDING, DOMAIN SWAPPING JRNL TITL 2 AND HEAT RESISTANCE OF A HYPERTHERMOSTABLE ARCHAEAL AIR JRNL TITL 3 SYNTHETASE. JRNL REF INT.J.BIOL.MACROMOL. V. 344 50493 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 41581817 JRNL DOI 10.1016/J.IJBIOMAC.2026.150493 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 99619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 5142 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 26.9300 - 4.9800 1.00 3240 182 0.1752 0.1771 REMARK 3 2 4.9800 - 3.9500 1.00 3204 174 0.1282 0.1416 REMARK 3 3 3.9500 - 3.4600 1.00 3173 175 0.1380 0.1491 REMARK 3 4 3.4500 - 3.1400 1.00 3177 190 0.1523 0.1638 REMARK 3 5 3.1400 - 2.9100 1.00 3171 186 0.1539 0.1689 REMARK 3 6 2.9100 - 2.7400 1.00 3186 158 0.1544 0.1825 REMARK 3 7 2.7400 - 2.6100 1.00 3178 153 0.1555 0.1594 REMARK 3 8 2.6100 - 2.4900 1.00 3183 172 0.1538 0.1647 REMARK 3 9 2.4900 - 2.4000 1.00 3147 166 0.1538 0.1837 REMARK 3 10 2.4000 - 2.3100 1.00 3199 168 0.1521 0.1569 REMARK 3 11 2.3100 - 2.2400 1.00 3160 141 0.1560 0.1881 REMARK 3 12 2.2400 - 2.1800 1.00 3167 160 0.1484 0.1877 REMARK 3 13 2.1800 - 2.1200 1.00 3174 168 0.1433 0.1673 REMARK 3 14 2.1200 - 2.0700 0.99 3135 190 0.1463 0.1784 REMARK 3 15 2.0700 - 2.0200 0.99 3166 159 0.1566 0.1926 REMARK 3 16 2.0200 - 1.9800 0.99 3138 177 0.1551 0.1667 REMARK 3 17 1.9800 - 1.9400 0.99 3141 184 0.1553 0.1915 REMARK 3 18 1.9400 - 1.9000 0.99 3075 187 0.1516 0.1817 REMARK 3 19 1.9000 - 1.8700 0.99 3150 174 0.1558 0.2041 REMARK 3 20 1.8700 - 1.8400 0.99 3150 180 0.1619 0.1945 REMARK 3 21 1.8400 - 1.8100 0.99 3104 179 0.1660 0.1849 REMARK 3 22 1.8100 - 1.7800 0.99 3145 187 0.1780 0.2086 REMARK 3 23 1.7800 - 1.7500 0.99 3117 166 0.1852 0.2388 REMARK 3 24 1.7500 - 1.7300 0.99 3083 188 0.2004 0.2443 REMARK 3 25 1.7300 - 1.7100 0.99 3162 150 0.2069 0.2663 REMARK 3 26 1.7100 - 1.6800 0.99 3137 154 0.1989 0.2264 REMARK 3 27 1.6800 - 1.6600 0.98 3116 157 0.2002 0.2466 REMARK 3 28 1.6600 - 1.6400 0.99 3125 166 0.2100 0.2165 REMARK 3 29 1.6400 - 1.6200 0.98 3117 160 0.2154 0.2402 REMARK 3 30 1.6200 - 1.6000 0.97 3057 191 0.2284 0.2699 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.92 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 5152 REMARK 3 ANGLE : 1.055 6980 REMARK 3 CHIRALITY : 0.063 794 REMARK 3 PLANARITY : 0.010 882 REMARK 3 DIHEDRAL : 12.660 724 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 9K04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-25 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 07A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS V20200131 REMARK 200 DATA SCALING SOFTWARE : XDS V20200131 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99620 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.77700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.21.2_5419 REMARK 200 STARTING MODEL: 9K00 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM CHLORIDE, PENTAERYTHRITOL REMARK 280 ETHOXYLATE, GLYCINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 51.48200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.10800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.48200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 56.10800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.0 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 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 ASN A 146 50.06 -99.31 REMARK 500 HIS A 184 -131.49 60.66 REMARK 500 THR A 241 -135.68 -122.61 REMARK 500 ASN B 146 37.02 -99.20 REMARK 500 HIS B 184 -129.65 56.19 REMARK 500 THR B 241 -130.78 -121.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 168 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 805 DISTANCE = 6.42 ANGSTROMS 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 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 45 O REMARK 620 2 THR A 59 OG1 73.5 REMARK 620 3 ASP A 90 OD2 87.7 83.0 REMARK 620 4 HOH A 538 O 164.3 110.6 107.7 REMARK 620 5 ADP B 402 O1B 90.5 163.2 91.8 86.2 REMARK 620 6 ADP B 402 O3B 128.3 138.0 65.3 59.2 50.3 REMARK 620 7 HOH B 656 O 103.9 71.5 147.1 64.7 118.3 123.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 61 OD2 REMARK 620 2 ASP A 90 OD2 82.9 REMARK 620 3 PO4 A 402 O2 99.7 174.4 REMARK 620 4 HOH A 548 O 88.4 96.0 79.1 REMARK 620 5 ADP B 402 O3B 90.6 96.1 88.9 167.6 REMARK 620 6 HOH B 507 O 166.1 84.1 92.8 88.0 95.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 61 OD1 REMARK 620 2 PO4 A 402 O4 97.6 REMARK 620 3 HOH A 538 O 86.0 174.9 REMARK 620 4 GLU B 137 OE1 82.4 89.8 94.3 REMARK 620 5 ADP B 402 O2A 162.9 86.8 90.7 81.1 REMARK 620 6 ADP B 402 O3B 105.5 89.4 86.1 172.0 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 137 OE1 REMARK 620 2 ADP A 401 O3B 173.7 REMARK 620 3 ADP A 401 O2A 83.0 90.8 REMARK 620 4 ASP B 61 OD1 82.7 103.5 165.1 REMARK 620 5 PO4 B 401 O4 90.3 89.8 88.3 95.8 REMARK 620 6 HOH B 543 O 92.3 87.3 90.0 86.6 176.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 405 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 OG1 REMARK 620 2 GLY A 242 O 92.2 REMARK 620 3 ASN A 247 OD1 89.2 76.6 REMARK 620 4 PO4 A 402 O3 70.0 90.5 155.3 REMARK 620 5 ADP B 402 O2B 82.1 169.8 94.7 95.5 REMARK 620 6 ADP B 402 O3A 119.9 143.7 117.0 85.8 45.4 REMARK 620 7 HOH B 536 O 176.3 84.6 88.2 111.9 100.7 63.7 REMARK 620 8 HOH B 600 O 122.7 80.6 141.4 53.5 109.6 68.3 58.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 401 O3B REMARK 620 2 HOH A 507 O 95.4 REMARK 620 3 ASP B 61 OD2 91.4 164.7 REMARK 620 4 ASP B 90 OD2 95.8 83.3 82.3 REMARK 620 5 PO4 B 401 O2 88.5 94.4 99.5 175.3 REMARK 620 6 HOH B 516 O 165.7 85.7 91.1 98.5 77.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 405 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 401 O2B REMARK 620 2 ADP A 401 O3A 45.9 REMARK 620 3 HOH A 635 O 98.9 63.7 REMARK 620 4 THR B 241 OG1 80.9 119.5 172.7 REMARK 620 5 GLY B 242 O 169.0 144.0 86.4 92.7 REMARK 620 6 ASN B 247 OD1 96.4 119.2 84.9 87.9 74.3 REMARK 620 7 PO4 B 401 O3 93.8 84.7 116.9 70.3 92.4 154.1 REMARK 620 8 HOH B 609 O 113.6 71.0 61.4 125.5 77.4 136.9 57.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 401 O1B REMARK 620 2 ADP A 401 O3B 50.6 REMARK 620 3 HOH A 672 O 120.5 125.3 REMARK 620 4 TYR B 45 O 90.5 127.4 103.7 REMARK 620 5 THR B 59 OG1 160.3 139.2 70.5 70.4 REMARK 620 6 ASP B 90 OD2 90.2 63.9 147.0 86.1 84.0 REMARK 620 7 HOH B 543 O 86.7 60.2 65.7 165.2 113.0 108.4 REMARK 620 N 1 2 3 4 5 6 DBREF 9K04 A 14 334 UNP Q9UY56 PUR5_PYRAB 14 334 DBREF 9K04 B 14 334 UNP Q9UY56 PUR5_PYRAB 14 334 SEQADV 9K04 ALA A 239 UNP Q9UY56 HIS 239 ENGINEERED MUTATION SEQADV 9K04 ALA B 239 UNP Q9UY56 HIS 239 ENGINEERED MUTATION SEQRES 1 A 321 THR ALA ARG ALA LEU ARG GLU ILE ILE ARG THR ALA ARG SEQRES 2 A 321 GLU THR PHE LYS LEU ARG LYS GLY LYS VAL GLY GLU PRO SEQRES 3 A 321 GLY ASP ILE GLY HIS TYR ALA ALA LEU LEU ASP PHE GLY SEQRES 4 A 321 ASN PHE TYR LEU ALA MET THR THR ASP GLY VAL GLY THR SEQRES 5 A 321 LYS VAL LEU VAL ALA GLU ALA VAL GLY LYS PHE ASP THR SEQRES 6 A 321 ILE GLY ILE ASP MET ILE ALA MET ASN VAL ASN ASP LEU SEQRES 7 A 321 LEU CYS VAL GLY ALA GLU PRO LEU ALA LEU VAL ASP TYR SEQRES 8 A 321 PHE ALA VAL LYS GLU PRO ASN GLU GLU VAL PHE LYS GLN SEQRES 9 A 321 VAL ALA LYS GLY LEU TYR LYS GLY ALA GLU GLU ALA GLY SEQRES 10 A 321 VAL ALA ILE VAL GLY GLY GLU THR ALA VAL MET PRO ASP SEQRES 11 A 321 LEU ILE ASN GLY TYR ASP LEU ALA GLY THR ALA ILE GLY SEQRES 12 A 321 ILE VAL GLU LYS GLY LYS VAL ILE THR GLY GLU ARG ILE SEQRES 13 A 321 ARG PRO GLY ASP SER VAL ILE GLY ILE SER SER SER GLY SEQRES 14 A 321 ILE HIS SER ASN GLY LEU THR LEU ALA ARG LYS LEU LEU SEQRES 15 A 321 ILE PRO LYS TYR GLY LEU ASP TYR GLU TYR GLU GLY ARG SEQRES 16 A 321 LYS LEU TRP GLU TRP LEU LEU GLU PRO THR ARG ILE TYR SEQRES 17 A 321 VAL ARG PRO ILE LEU GLU LEU ILE ASN SER VAL GLU VAL SEQRES 18 A 321 HIS GLY LEU ALA ALA ILE THR GLY GLY GLY LEU LEU ASN SEQRES 19 A 321 LEU LYS ARG LEU THR ASN TYR GLY PHE GLU LEU GLU MET SEQRES 20 A 321 PRO PRO ILE GLU GLY ILE PHE LYS LEU ILE HIS GLU ASN SEQRES 21 A 321 GLY VAL PRO LEU ASP GLU MET PHE ARG VAL PHE ASN MET SEQRES 22 A 321 GLY VAL GLY PHE ILE VAL VAL VAL PRO GLN GLU GLU LYS SEQRES 23 A 321 GLU GLU ALA LEU GLU ILE LEU SER ARG HIS TYR LYS SER SEQRES 24 A 321 TYR GLU LEU GLY ASN VAL THR ARG GLU LEU GLY LYS ILE SEQRES 25 A 321 LYS VAL LYS ASN TYR GLY ILE THR LEU SEQRES 1 B 321 THR ALA ARG ALA LEU ARG GLU ILE ILE ARG THR ALA ARG SEQRES 2 B 321 GLU THR PHE LYS LEU ARG LYS GLY LYS VAL GLY GLU PRO SEQRES 3 B 321 GLY ASP ILE GLY HIS TYR ALA ALA LEU LEU ASP PHE GLY SEQRES 4 B 321 ASN PHE TYR LEU ALA MET THR THR ASP GLY VAL GLY THR SEQRES 5 B 321 LYS VAL LEU VAL ALA GLU ALA VAL GLY LYS PHE ASP THR SEQRES 6 B 321 ILE GLY ILE ASP MET ILE ALA MET ASN VAL ASN ASP LEU SEQRES 7 B 321 LEU CYS VAL GLY ALA GLU PRO LEU ALA LEU VAL ASP TYR SEQRES 8 B 321 PHE ALA VAL LYS GLU PRO ASN GLU GLU VAL PHE LYS GLN SEQRES 9 B 321 VAL ALA LYS GLY LEU TYR LYS GLY ALA GLU GLU ALA GLY SEQRES 10 B 321 VAL ALA ILE VAL GLY GLY GLU THR ALA VAL MET PRO ASP SEQRES 11 B 321 LEU ILE ASN GLY TYR ASP LEU ALA GLY THR ALA ILE GLY SEQRES 12 B 321 ILE VAL GLU LYS GLY LYS VAL ILE THR GLY GLU ARG ILE SEQRES 13 B 321 ARG PRO GLY ASP SER VAL ILE GLY ILE SER SER SER GLY SEQRES 14 B 321 ILE HIS SER ASN GLY LEU THR LEU ALA ARG LYS LEU LEU SEQRES 15 B 321 ILE PRO LYS TYR GLY LEU ASP TYR GLU TYR GLU GLY ARG SEQRES 16 B 321 LYS LEU TRP GLU TRP LEU LEU GLU PRO THR ARG ILE TYR SEQRES 17 B 321 VAL ARG PRO ILE LEU GLU LEU ILE ASN SER VAL GLU VAL SEQRES 18 B 321 HIS GLY LEU ALA ALA ILE THR GLY GLY GLY LEU LEU ASN SEQRES 19 B 321 LEU LYS ARG LEU THR ASN TYR GLY PHE GLU LEU GLU MET SEQRES 20 B 321 PRO PRO ILE GLU GLY ILE PHE LYS LEU ILE HIS GLU ASN SEQRES 21 B 321 GLY VAL PRO LEU ASP GLU MET PHE ARG VAL PHE ASN MET SEQRES 22 B 321 GLY VAL GLY PHE ILE VAL VAL VAL PRO GLN GLU GLU LYS SEQRES 23 B 321 GLU GLU ALA LEU GLU ILE LEU SER ARG HIS TYR LYS SER SEQRES 24 B 321 TYR GLU LEU GLY ASN VAL THR ARG GLU LEU GLY LYS ILE SEQRES 25 B 321 LYS VAL LYS ASN TYR GLY ILE THR LEU HET ADP A 401 27 HET PO4 A 402 5 HET MN A 403 1 HET MN A 404 1 HET K A 405 1 HET K A 406 1 HET PO4 B 401 5 HET ADP B 402 27 HET MN B 403 1 HET MN B 404 1 HET K B 405 1 HET K B 406 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 MN 4(MN 2+) FORMUL 7 K 4(K 1+) FORMUL 15 HOH *575(H2 O) HELIX 1 AA1 THR A 14 PHE A 29 1 16 HELIX 2 AA2 LYS A 30 LYS A 33 5 4 HELIX 3 AA3 THR A 65 GLY A 74 1 10 HELIX 4 AA4 THR A 78 CYS A 93 1 16 HELIX 5 AA5 ASN A 111 GLY A 130 1 20 HELIX 6 AA6 GLY A 187 GLY A 200 1 14 HELIX 7 AA7 LEU A 210 GLU A 216 1 7 HELIX 8 AA8 TYR A 221 ASN A 230 1 10 HELIX 9 AA9 GLY A 243 LEU A 251 5 9 HELIX 10 AB1 GLU A 264 GLU A 272 1 9 HELIX 11 AB2 PRO A 276 PHE A 284 1 9 HELIX 12 AB3 PRO A 295 GLU A 297 5 3 HELIX 13 AB4 GLU A 298 ARG A 308 1 11 HELIX 14 AB5 ASN A 329 GLY A 331 5 3 HELIX 15 AB6 ALA B 15 PHE B 29 1 15 HELIX 16 AB7 LYS B 30 LYS B 33 5 4 HELIX 17 AB8 THR B 65 GLY B 74 1 10 HELIX 18 AB9 THR B 78 CYS B 93 1 16 HELIX 19 AC1 ASN B 111 GLY B 130 1 20 HELIX 20 AC2 GLY B 187 GLY B 200 1 14 HELIX 21 AC3 LEU B 210 GLU B 216 1 7 HELIX 22 AC4 TYR B 221 ASN B 230 1 10 HELIX 23 AC5 GLY B 243 LEU B 251 5 9 HELIX 24 AC6 GLU B 264 ASN B 273 1 10 HELIX 25 AC7 PRO B 276 PHE B 284 1 9 HELIX 26 AC8 PRO B 295 GLU B 297 5 3 HELIX 27 AC9 GLU B 298 ARG B 308 1 11 HELIX 28 AD1 ASN B 329 GLY B 331 5 3 SHEET 1 AA1 6 GLU A 38 PRO A 39 0 SHEET 2 AA1 6 ALA A 47 ASP A 50 -1 O ASP A 50 N GLU A 38 SHEET 3 AA1 6 PHE A 54 GLY A 62 -1 O MET A 58 N ALA A 47 SHEET 4 AA1 6 TYR A 148 GLU A 159 -1 O VAL A 158 N TYR A 55 SHEET 5 AA1 6 GLU A 97 VAL A 107 -1 N ALA A 106 O ASP A 149 SHEET 6 AA1 6 ALA A 132 VAL A 140 1 O GLU A 137 N PHE A 105 SHEET 1 AA2 7 GLY A 236 ALA A 239 0 SHEET 2 AA2 7 VAL A 288 VAL A 294 -1 O ILE A 291 N ALA A 238 SHEET 3 AA2 7 SER A 174 SER A 179 -1 N ILE A 176 O VAL A 292 SHEET 4 AA2 7 SER A 312 THR A 319 -1 O TYR A 313 N GLY A 177 SHEET 5 AA2 7 GLY A 255 LEU A 258 -1 N GLU A 257 O ASN A 317 SHEET 6 AA2 7 ILE A 325 VAL A 327 1 O LYS A 326 N LEU A 258 SHEET 7 AA2 7 ILE A 332 LEU A 334 -1 O ILE A 332 N VAL A 327 SHEET 1 AA3 2 GLU A 204 TYR A 205 0 SHEET 2 AA3 2 ARG A 208 LYS A 209 -1 O ARG A 208 N TYR A 205 SHEET 1 AA4 6 GLU B 38 PRO B 39 0 SHEET 2 AA4 6 ALA B 47 ASP B 50 -1 O ASP B 50 N GLU B 38 SHEET 3 AA4 6 PHE B 54 GLY B 62 -1 O MET B 58 N ALA B 47 SHEET 4 AA4 6 TYR B 148 GLU B 159 -1 O VAL B 158 N TYR B 55 SHEET 5 AA4 6 GLU B 97 VAL B 107 -1 N TYR B 104 O ALA B 151 SHEET 6 AA4 6 ALA B 132 VAL B 140 1 O GLU B 137 N PHE B 105 SHEET 1 AA5 7 GLY B 236 ALA B 239 0 SHEET 2 AA5 7 VAL B 288 VAL B 294 -1 O ILE B 291 N ALA B 238 SHEET 3 AA5 7 SER B 174 SER B 179 -1 N ILE B 178 O PHE B 290 SHEET 4 AA5 7 SER B 312 LEU B 322 -1 O TYR B 313 N GLY B 177 SHEET 5 AA5 7 TYR B 254 LEU B 258 -1 N GLY B 255 O THR B 319 SHEET 6 AA5 7 ILE B 325 VAL B 327 1 O LYS B 326 N LEU B 258 SHEET 7 AA5 7 ILE B 332 THR B 333 -1 O ILE B 332 N VAL B 327 SHEET 1 AA6 2 GLU B 204 TYR B 205 0 SHEET 2 AA6 2 ARG B 208 LYS B 209 -1 O ARG B 208 N TYR B 205 LINK O TYR A 45 K K A 406 1555 1555 2.73 LINK OG1 THR A 59 K K A 406 1555 1555 2.66 LINK OD2 ASP A 61 MN MN A 403 1555 1555 2.15 LINK OD1 ASP A 61 MN MN A 404 1555 1555 2.19 LINK OD2 ASP A 90 MN MN A 403 1555 1555 2.19 LINK OD2 ASP A 90 K K A 406 1555 1555 2.91 LINK OE1 GLU A 137 MN MN B 404 1555 1555 2.19 LINK OG1 THR A 241 K K A 405 1555 1555 2.97 LINK O GLY A 242 K K A 405 1555 1555 2.74 LINK OD1 ASN A 247 K K A 405 1555 1555 2.90 LINK O3B ADP A 401 MN MN B 403 1555 1555 2.17 LINK O3B ADP A 401 MN MN B 404 1555 1555 2.28 LINK O2A ADP A 401 MN MN B 404 1555 1555 2.03 LINK O2B ADP A 401 K K B 405 1555 1555 2.79 LINK O3A ADP A 401 K K B 405 1555 1555 3.24 LINK O1B ADP A 401 K K B 406 1555 1555 2.76 LINK O3B ADP A 401 K K B 406 1555 1555 3.15 LINK O2 PO4 A 402 MN MN A 403 1555 1555 2.06 LINK O4 PO4 A 402 MN MN A 404 1555 1555 2.09 LINK O3 PO4 A 402 K K A 405 1555 1555 2.75 LINK MN MN A 403 O HOH A 548 1555 1555 2.20 LINK MN MN A 403 O3B ADP B 402 1555 1555 2.20 LINK MN MN A 403 O HOH B 507 1555 1555 2.20 LINK MN MN A 404 O HOH A 538 1555 1555 2.20 LINK MN MN A 404 OE1 GLU B 137 1555 1555 2.16 LINK MN MN A 404 O2A ADP B 402 1555 1555 2.09 LINK MN MN A 404 O3B ADP B 402 1555 1555 2.28 LINK K K A 405 O2B ADP B 402 1555 1555 2.76 LINK K K A 405 O3A ADP B 402 1555 1555 3.24 LINK K K A 405 O HOH B 536 1555 1555 2.77 LINK K K A 405 O HOH B 600 1555 1555 3.43 LINK K K A 406 O HOH A 538 1555 1555 3.06 LINK K K A 406 O1B ADP B 402 1555 1555 2.77 LINK K K A 406 O3B ADP B 402 1555 1555 3.13 LINK K K A 406 O HOH B 656 1555 1555 3.01 LINK O HOH A 507 MN MN B 403 1555 1555 2.22 LINK O HOH A 635 K K B 405 1555 1555 2.98 LINK O HOH A 672 K K B 406 1555 1555 2.97 LINK O TYR B 45 K K B 406 1555 1555 2.76 LINK OG1 THR B 59 K K B 406 1555 1555 2.70 LINK OD2 ASP B 61 MN MN B 403 1555 1555 2.10 LINK OD1 ASP B 61 MN MN B 404 1555 1555 2.20 LINK OD2 ASP B 90 MN MN B 403 1555 1555 2.18 LINK OD2 ASP B 90 K K B 406 1555 1555 2.93 LINK OG1 THR B 241 K K B 405 1555 1555 3.03 LINK O GLY B 242 K K B 405 1555 1555 2.88 LINK OD1 ASN B 247 K K B 405 1555 1555 2.80 LINK O2 PO4 B 401 MN MN B 403 1555 1555 2.06 LINK O4 PO4 B 401 MN MN B 404 1555 1555 2.06 LINK O3 PO4 B 401 K K B 405 1555 1555 2.67 LINK MN MN B 403 O HOH B 516 1555 1555 2.19 LINK MN MN B 404 O HOH B 543 1555 1555 2.21 LINK K K B 405 O HOH B 609 1555 1555 3.20 LINK K K B 406 O HOH B 543 1555 1555 3.03 CRYST1 102.964 112.216 70.512 90.00 105.82 90.00 C 1 2 1 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 0.009712 0.000000 0.002751 0.00000 SCALE2 0.000000 0.008911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014740 0.00000 CONECT 258 5032 CONECT 373 5032 CONECT 388 5030 CONECT 389 5029 CONECT 595 5029 5032 CONECT 940 5066 CONECT 1743 5031 CONECT 1748 5031 CONECT 1779 5031 CONECT 2756 5068 CONECT 2871 5068 CONECT 2886 5066 CONECT 2887 5065 CONECT 3093 5065 5068 CONECT 3438 5030 CONECT 4241 5067 CONECT 4246 5067 CONECT 4277 5067 CONECT 4997 4998 4999 5000 5004 CONECT 4998 4997 5068 CONECT 4999 4997 5067 CONECT 5000 4997 5065 5066 5068 CONECT 5001 5002 5003 5004 5005 CONECT 5002 5001 CONECT 5003 5001 5066 CONECT 5004 4997 5001 5067 CONECT 5005 5001 5006 CONECT 5006 5005 5007 CONECT 5007 5006 5008 5009 CONECT 5008 5007 5013 CONECT 5009 5007 5010 5011 CONECT 5010 5009 CONECT 5011 5009 5012 5013 CONECT 5012 5011 CONECT 5013 5008 5011 5014 CONECT 5014 5013 5015 5023 CONECT 5015 5014 5016 CONECT 5016 5015 5017 CONECT 5017 5016 5018 5023 CONECT 5018 5017 5019 5020 CONECT 5019 5018 CONECT 5020 5018 5021 CONECT 5021 5020 5022 CONECT 5022 5021 5023 CONECT 5023 5014 5017 5022 CONECT 5024 5025 5026 5027 5028 CONECT 5025 5024 CONECT 5026 5024 5029 CONECT 5027 5024 5031 CONECT 5028 5024 5030 CONECT 5029 389 595 5026 5041 CONECT 5029 5116 5380 CONECT 5030 388 3438 5028 5041 CONECT 5030 5044 5106 CONECT 5031 1743 1748 1779 5027 CONECT 5031 5040 5045 5409 5473 CONECT 5032 258 373 595 5039 CONECT 5032 5041 5106 5529 CONECT 5033 5034 5035 5036 5037 CONECT 5034 5033 CONECT 5035 5033 5065 CONECT 5036 5033 5067 CONECT 5037 5033 5066 CONECT 5038 5039 5040 5041 5045 CONECT 5039 5032 5038 CONECT 5040 5031 5038 CONECT 5041 5029 5030 5032 5038 CONECT 5042 5043 5044 5045 5046 CONECT 5043 5042 CONECT 5044 5030 5042 CONECT 5045 5031 5038 5042 CONECT 5046 5042 5047 CONECT 5047 5046 5048 CONECT 5048 5047 5049 5050 CONECT 5049 5048 5054 CONECT 5050 5048 5051 5052 CONECT 5051 5050 CONECT 5052 5050 5053 5054 CONECT 5053 5052 CONECT 5054 5049 5052 5055 CONECT 5055 5054 5056 5064 CONECT 5056 5055 5057 CONECT 5057 5056 5058 CONECT 5058 5057 5059 5064 CONECT 5059 5058 5060 5061 CONECT 5060 5059 CONECT 5061 5059 5062 CONECT 5062 5061 5063 CONECT 5063 5062 5064 CONECT 5064 5055 5058 5063 CONECT 5065 2887 3093 5000 5035 CONECT 5065 5075 5389 CONECT 5066 940 2886 5000 5003 CONECT 5066 5037 5416 CONECT 5067 4241 4246 4277 4999 CONECT 5067 5004 5036 5203 5482 CONECT 5068 2756 2871 3093 4998 CONECT 5068 5000 5240 5416 CONECT 5075 5065 CONECT 5106 5030 5032 CONECT 5116 5029 CONECT 5203 5067 CONECT 5240 5068 CONECT 5380 5029 CONECT 5389 5065 CONECT 5409 5031 CONECT 5416 5066 5068 CONECT 5473 5031 CONECT 5482 5067 CONECT 5529 5032 MASTER 372 0 12 28 30 0 0 6 5605 2 110 50 END