HEADER LIGASE 10-MAR-22 7U9K TITLE STAPHYLOCOCCUS AUREUS D-ALANINE-D-ALANINE LIGASE IN COMPLEX WITH ATP, TITLE 2 D-ALA-D-ALA, MG2+ AND K+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE--D-ALANINE LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D-ALA-D-ALA LIGASE,D-ALANYLALANINE SYNTHETASE; COMPND 5 EC: 6.3.2.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DAL-DAL; COMPND 9 CHAIN: F; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: D-ALANINE-D-ALANINE DIPEPTIDE PRODUCT FORMED BY D- COMPND 12 ALANINE-D-ALANINE LIGASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325 / PS 47; SOURCE 5 GENE: DDL, SAOUHSC_02318; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 11 ORGANISM_TAXID: 93061 KEYWDS ATP-GRASP, NUCLEOTIDE BINDING, METAL BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.PEDERICK,J.B.BRUNING REVDAT 3 31-JAN-24 7U9K 1 JRNL REVDAT 2 25-OCT-23 7U9K 1 REMARK REVDAT 1 15-MAR-23 7U9K 0 JRNL AUTH R.BECKER,J.L.PEDERICK,E.G.DAWES,J.B.BRUNING,A.D.ABELL JRNL TITL STRUCTURE-GUIDED DESIGN AND SYNTHESIS OF ATP-COMPETITIVE JRNL TITL 2 N-ACYL-SUBSTITUTED SULFAMIDE D-ALANINE-D-ALANINE LIGASE JRNL TITL 3 INHIBITORS. JRNL REF BIOORG.MED.CHEM. V. 96 17509 2023 JRNL REFN ESSN 1464-3391 JRNL PMID 37948922 JRNL DOI 10.1016/J.BMC.2023.117509 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 43840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2160 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 37.6800 - 4.9300 1.00 2840 171 0.2012 0.2188 REMARK 3 2 4.9300 - 3.9100 0.99 2784 143 0.1895 0.2303 REMARK 3 3 3.9100 - 3.4200 1.00 2767 168 0.2227 0.2742 REMARK 3 4 3.4200 - 3.1100 1.00 2791 145 0.2501 0.2579 REMARK 3 5 3.1100 - 2.8800 1.00 2792 111 0.2605 0.3251 REMARK 3 6 2.8800 - 2.7100 1.00 2817 142 0.2618 0.3147 REMARK 3 7 2.7100 - 2.5800 1.00 2710 159 0.2757 0.3112 REMARK 3 8 2.5800 - 2.4700 1.00 2780 157 0.2671 0.3210 REMARK 3 9 2.4700 - 2.3700 1.00 2767 135 0.2675 0.3032 REMARK 3 10 2.3700 - 2.2900 1.00 2764 135 0.2652 0.3225 REMARK 3 11 2.2900 - 2.2200 1.00 2777 149 0.2713 0.3074 REMARK 3 12 2.2200 - 2.1500 1.00 2825 123 0.2759 0.3261 REMARK 3 13 2.1500 - 2.1000 1.00 2723 133 0.2635 0.3481 REMARK 3 14 2.1000 - 2.0500 1.00 2777 147 0.2842 0.3026 REMARK 3 15 2.0500 - 2.0000 1.00 2766 142 0.3081 0.3674 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7U9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-18 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 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 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.21600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.69300 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: PHASER 2.8.3 REMARK 200 STARTING MODEL: 2I87 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 - 30% PEG 3350, 0.5 M KCL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.02900 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F 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 THR A 2 REMARK 465 ASN A 69 REMARK 465 GLY A 70 REMARK 465 GLU A 71 REMARK 465 ALA A 72 REMARK 465 LYS A 241 REMARK 465 ASP A 242 REMARK 465 VAL A 243 REMARK 465 ALA A 244 REMARK 465 PHE A 245 REMARK 465 TYR A 246 REMARK 465 ASP A 247 REMARK 465 TYR A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 LYS A 251 REMARK 465 TYR A 252 REMARK 465 LYS A 253 REMARK 465 ASP A 254 REMARK 465 GLY A 255 REMARK 465 LYS A 256 REMARK 465 ILE A 355 REMARK 465 ASP A 356 REMARK 465 ARG A 357 REMARK 465 SER A 358 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 465 HIS A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ASP B 32 REMARK 465 LYS B 33 REMARK 465 ASP B 34 REMARK 465 LYS B 35 REMARK 465 GLU B 68 REMARK 465 ASN B 69 REMARK 465 GLY B 70 REMARK 465 GLU B 71 REMARK 465 ALA B 72 REMARK 465 LEU B 73 REMARK 465 LYS B 80 REMARK 465 GLU B 81 REMARK 465 SER B 82 REMARK 465 SER B 83 REMARK 465 SER B 84 REMARK 465 GLY B 85 REMARK 465 LYS B 350 REMARK 465 ASN B 351 REMARK 465 LYS B 352 REMARK 465 TYR B 353 REMARK 465 LYS B 354 REMARK 465 ILE B 355 REMARK 465 ASP B 356 REMARK 465 ARG B 357 REMARK 465 SER B 358 REMARK 465 HIS B 359 REMARK 465 HIS B 360 REMARK 465 HIS B 361 REMARK 465 HIS B 362 REMARK 465 HIS B 363 REMARK 465 HIS B 364 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 16 CG CD OE1 OE2 REMARK 470 ASN A 45 CG OD1 ND2 REMARK 470 LEU A 73 CG CD1 CD2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 GLN A 205 CG CD OE1 NE2 REMARK 470 PHE A 206 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 230 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 240 CG1 CG2 REMARK 470 VAL A 257 CG1 CG2 REMARK 470 GLN A 258 CG CD OE1 NE2 REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 LYS A 348 CG CD CE NZ REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 ILE B 6 CG1 CG2 CD1 REMARK 470 LEU B 22 CG CD1 CD2 REMARK 470 HIS B 37 CG ND1 CD2 CE1 NE2 REMARK 470 ASN B 54 CG OD1 ND2 REMARK 470 THR B 56 OG1 CG2 REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 GLN B 86 CG CD OE1 NE2 REMARK 470 LYS B 157 CG CD CE NZ REMARK 470 GLU B 232 CG CD OE1 OE2 REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 LYS B 253 CG CD CE NZ REMARK 470 LYS B 256 CG CD CE NZ REMARK 470 GLN B 258 CG CD OE1 NE2 REMARK 470 GLU B 267 CG CD OE1 OE2 REMARK 470 GLU B 332 CG CD OE1 OE2 REMARK 470 LYS B 342 CG CD CE NZ REMARK 470 GLN B 346 CG CD OE1 NE2 REMARK 470 LYS B 348 CG CD CE NZ 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 GLU A 16 37.56 -89.83 REMARK 500 ASN A 54 80.63 57.75 REMARK 500 ASN A 228 -78.02 -111.20 REMARK 500 GLU B 16 32.63 -92.01 REMARK 500 ASN B 54 94.83 56.87 REMARK 500 ALA B 90 137.60 -173.06 REMARK 500 ASN B 228 -97.69 -109.21 REMARK 500 ASN B 300 32.27 70.00 REMARK 500 ASN B 305 -65.08 -96.98 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 669 DISTANCE = 10.01 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 B 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 63 O REMARK 620 2 HIS A 66 O 88.2 REMARK 620 3 HOH A 613 O 58.3 32.4 REMARK 620 4 ASN B 171 OD1 55.9 33.5 3.9 REMARK 620 5 TYR B 172 O 58.7 31.2 2.2 2.9 REMARK 620 6 HOH B 549 O 55.6 34.6 2.8 2.3 3.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 127 O REMARK 620 2 GLU A 306 OE1 129.1 REMARK 620 3 THR A 307 O 97.5 93.4 REMARK 620 4 HOH A 507 O 153.9 76.6 83.3 REMARK 620 5 HOH A 555 O 83.0 147.4 74.4 72.1 REMARK 620 6 HOH A 611 O 67.8 71.6 139.1 126.8 136.1 REMARK 620 7 HOH A 654 O 94.7 84.7 165.6 82.4 99.6 53.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 306 OE2 REMARK 620 2 ADP A 403 O1B 101.7 REMARK 620 3 ADP A 403 O1A 89.0 93.7 REMARK 620 4 HOH A 543 O 77.8 174.0 80.3 REMARK 620 5 HOH A 586 O 83.1 89.5 172.0 96.4 REMARK 620 6 HOH A 609 O 170.0 88.3 89.7 92.2 97.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 127 O REMARK 620 2 GLU B 306 OE1 135.4 REMARK 620 3 THR B 307 O 86.7 83.2 REMARK 620 4 ASN B 308 OD1 151.8 61.9 72.3 REMARK 620 5 HOH B 507 O 96.4 82.7 162.8 109.2 REMARK 620 6 HOH B 535 O 148.9 67.8 120.6 48.4 62.2 REMARK 620 7 HOH B 579 O 85.4 136.2 84.7 74.3 112.4 83.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD2 REMARK 620 2 GLU B 306 OE2 78.1 REMARK 620 3 ATP B 405 O2A 127.4 65.4 REMARK 620 4 ATP B 405 O3G 92.0 71.7 109.6 REMARK 620 5 ATP B 405 O3B 130.9 61.5 59.9 51.0 REMARK 620 6 HOH B 519 O 139.1 137.6 91.5 85.0 76.2 REMARK 620 7 HOH B 551 O 93.6 124.8 138.1 54.0 88.1 52.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 306 OE1 REMARK 620 2 GLU B 306 OE2 56.1 REMARK 620 3 ASN B 308 OD1 92.9 94.5 REMARK 620 4 ATP B 405 O2G 151.8 99.0 102.8 REMARK 620 5 ATP B 405 O2B 75.4 77.8 168.3 87.3 REMARK 620 6 HOH B 535 O 99.6 155.4 82.5 105.5 100.8 REMARK 620 N 1 2 3 4 5 DBREF 7U9K A 1 356 UNP Q2FWH3 DDL_STAA8 1 356 DBREF 7U9K B 1 356 UNP Q2FWH3 DDL_STAA8 1 356 DBREF 7U9K F 1 2 PDB 7U9K 7U9K 1 2 SEQADV 7U9K ARG A 357 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K SER A 358 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 359 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 360 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 361 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 362 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 363 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS A 364 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K ARG B 357 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K SER B 358 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 359 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 360 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 361 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 362 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 363 UNP Q2FWH3 EXPRESSION TAG SEQADV 7U9K HIS B 364 UNP Q2FWH3 EXPRESSION TAG SEQRES 1 A 364 MET THR LYS GLU ASN ILE CYS ILE VAL PHE GLY GLY LYS SEQRES 2 A 364 SER ALA GLU HIS GLU VAL SER ILE LEU THR ALA GLN ASN SEQRES 3 A 364 VAL LEU ASN ALA ILE ASP LYS ASP LYS TYR HIS VAL ASP SEQRES 4 A 364 ILE ILE TYR ILE THR ASN ASP GLY ASP TRP ARG LYS GLN SEQRES 5 A 364 ASN ASN ILE THR ALA GLU ILE LYS SER THR ASP GLU LEU SEQRES 6 A 364 HIS LEU GLU ASN GLY GLU ALA LEU GLU ILE SER GLN LEU SEQRES 7 A 364 LEU LYS GLU SER SER SER GLY GLN PRO TYR ASP ALA VAL SEQRES 8 A 364 PHE PRO LEU LEU HIS GLY PRO ASN GLY GLU ASP GLY THR SEQRES 9 A 364 ILE GLN GLY LEU PHE GLU VAL LEU ASP VAL PRO TYR VAL SEQRES 10 A 364 GLY ASN GLY VAL LEU SER ALA ALA SER SER MET ASP LYS SEQRES 11 A 364 LEU VAL MET LYS GLN LEU PHE GLU HIS ARG GLY LEU PRO SEQRES 12 A 364 GLN LEU PRO TYR ILE SER PHE LEU ARG SER GLU TYR GLU SEQRES 13 A 364 LYS TYR GLU HIS ASN ILE LEU LYS LEU VAL ASN ASP LYS SEQRES 14 A 364 LEU ASN TYR PRO VAL PHE VAL LYS PRO ALA ASN LEU GLY SEQRES 15 A 364 SER SER VAL GLY ILE SER LYS CYS ASN ASN GLU ALA GLU SEQRES 16 A 364 LEU LYS GLU GLY ILE LYS GLU ALA PHE GLN PHE ASP ARG SEQRES 17 A 364 LYS LEU VAL ILE GLU GLN GLY VAL ASN ALA ARG GLU ILE SEQRES 18 A 364 GLU VAL ALA VAL LEU GLY ASN ASP TYR PRO GLU ALA THR SEQRES 19 A 364 TRP PRO GLY GLU VAL VAL LYS ASP VAL ALA PHE TYR ASP SEQRES 20 A 364 TYR LYS SER LYS TYR LYS ASP GLY LYS VAL GLN LEU GLN SEQRES 21 A 364 ILE PRO ALA ASP LEU ASP GLU ASP VAL GLN LEU THR LEU SEQRES 22 A 364 ARG ASN MET ALA LEU GLU ALA PHE LYS ALA THR ASP CYS SEQRES 23 A 364 SER GLY LEU VAL ARG ALA ASP PHE PHE VAL THR GLU ASP SEQRES 24 A 364 ASN GLN ILE TYR ILE ASN GLU THR ASN ALA MET PRO GLY SEQRES 25 A 364 PHE THR ALA PHE SER MET TYR PRO LYS LEU TRP GLU ASN SEQRES 26 A 364 MET GLY LEU SER TYR PRO GLU LEU ILE THR LYS LEU ILE SEQRES 27 A 364 GLU LEU ALA LYS GLU ARG HIS GLN ASP LYS GLN LYS ASN SEQRES 28 A 364 LYS TYR LYS ILE ASP ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 364 MET THR LYS GLU ASN ILE CYS ILE VAL PHE GLY GLY LYS SEQRES 2 B 364 SER ALA GLU HIS GLU VAL SER ILE LEU THR ALA GLN ASN SEQRES 3 B 364 VAL LEU ASN ALA ILE ASP LYS ASP LYS TYR HIS VAL ASP SEQRES 4 B 364 ILE ILE TYR ILE THR ASN ASP GLY ASP TRP ARG LYS GLN SEQRES 5 B 364 ASN ASN ILE THR ALA GLU ILE LYS SER THR ASP GLU LEU SEQRES 6 B 364 HIS LEU GLU ASN GLY GLU ALA LEU GLU ILE SER GLN LEU SEQRES 7 B 364 LEU LYS GLU SER SER SER GLY GLN PRO TYR ASP ALA VAL SEQRES 8 B 364 PHE PRO LEU LEU HIS GLY PRO ASN GLY GLU ASP GLY THR SEQRES 9 B 364 ILE GLN GLY LEU PHE GLU VAL LEU ASP VAL PRO TYR VAL SEQRES 10 B 364 GLY ASN GLY VAL LEU SER ALA ALA SER SER MET ASP LYS SEQRES 11 B 364 LEU VAL MET LYS GLN LEU PHE GLU HIS ARG GLY LEU PRO SEQRES 12 B 364 GLN LEU PRO TYR ILE SER PHE LEU ARG SER GLU TYR GLU SEQRES 13 B 364 LYS TYR GLU HIS ASN ILE LEU LYS LEU VAL ASN ASP LYS SEQRES 14 B 364 LEU ASN TYR PRO VAL PHE VAL LYS PRO ALA ASN LEU GLY SEQRES 15 B 364 SER SER VAL GLY ILE SER LYS CYS ASN ASN GLU ALA GLU SEQRES 16 B 364 LEU LYS GLU GLY ILE LYS GLU ALA PHE GLN PHE ASP ARG SEQRES 17 B 364 LYS LEU VAL ILE GLU GLN GLY VAL ASN ALA ARG GLU ILE SEQRES 18 B 364 GLU VAL ALA VAL LEU GLY ASN ASP TYR PRO GLU ALA THR SEQRES 19 B 364 TRP PRO GLY GLU VAL VAL LYS ASP VAL ALA PHE TYR ASP SEQRES 20 B 364 TYR LYS SER LYS TYR LYS ASP GLY LYS VAL GLN LEU GLN SEQRES 21 B 364 ILE PRO ALA ASP LEU ASP GLU ASP VAL GLN LEU THR LEU SEQRES 22 B 364 ARG ASN MET ALA LEU GLU ALA PHE LYS ALA THR ASP CYS SEQRES 23 B 364 SER GLY LEU VAL ARG ALA ASP PHE PHE VAL THR GLU ASP SEQRES 24 B 364 ASN GLN ILE TYR ILE ASN GLU THR ASN ALA MET PRO GLY SEQRES 25 B 364 PHE THR ALA PHE SER MET TYR PRO LYS LEU TRP GLU ASN SEQRES 26 B 364 MET GLY LEU SER TYR PRO GLU LEU ILE THR LYS LEU ILE SEQRES 27 B 364 GLU LEU ALA LYS GLU ARG HIS GLN ASP LYS GLN LYS ASN SEQRES 28 B 364 LYS TYR LYS ILE ASP ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 F 2 DAL DAL HET DAL F 1 5 HET DAL F 2 6 HET K A 401 1 HET MG A 402 1 HET ADP A 403 27 HET K B 401 1 HET K B 402 1 HET K B 403 1 HET MG B 404 1 HET ATP B 405 31 HETNAM DAL D-ALANINE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 DAL 2(C3 H7 N O2) FORMUL 4 K 4(K 1+) FORMUL 5 MG 2(MG 2+) FORMUL 6 ADP C10 H15 N5 O10 P2 FORMUL 11 ATP C10 H16 N5 O13 P3 FORMUL 12 HOH *282(H2 O) HELIX 1 AA1 GLU A 16 ILE A 31 1 16 HELIX 2 AA2 SER A 61 HIS A 66 5 6 HELIX 3 AA3 GLU A 74 GLU A 81 1 8 HELIX 4 AA4 GLY A 103 ASP A 113 1 11 HELIX 5 AA5 GLY A 120 ASP A 129 1 10 HELIX 6 AA6 ASP A 129 GLY A 141 1 13 HELIX 7 AA7 ARG A 152 LEU A 170 1 19 HELIX 8 AA8 ASN A 192 GLN A 205 1 14 HELIX 9 AA9 ASP A 266 THR A 284 1 19 HELIX 10 AB1 SER A 317 MET A 326 1 10 HELIX 11 AB2 SER A 329 LYS A 350 1 22 HELIX 12 AB3 GLU B 16 ILE B 31 1 16 HELIX 13 AB4 THR B 62 HIS B 66 5 5 HELIX 14 AB5 ILE B 75 LEU B 79 1 5 HELIX 15 AB6 GLY B 103 LEU B 112 1 10 HELIX 16 AB7 GLY B 120 ASP B 129 1 10 HELIX 17 AB8 ASP B 129 GLY B 141 1 13 HELIX 18 AB9 ARG B 152 TYR B 158 1 7 HELIX 19 AC1 TYR B 158 LEU B 170 1 13 HELIX 20 AC2 ASN B 192 PHE B 204 1 13 HELIX 21 AC3 ASP B 247 LYS B 253 1 7 HELIX 22 AC4 ASP B 266 THR B 284 1 19 HELIX 23 AC5 MET B 318 ASN B 325 1 8 HELIX 24 AC6 SER B 329 GLN B 349 1 21 SHEET 1 AA1 4 TRP A 49 GLN A 52 0 SHEET 2 AA1 4 TYR A 36 ILE A 43 -1 N TYR A 42 O ARG A 50 SHEET 3 AA1 4 GLU A 4 GLY A 11 1 N GLU A 4 O HIS A 37 SHEET 4 AA1 4 ALA A 90 PRO A 93 1 O PHE A 92 N CYS A 7 SHEET 1 AA2 4 TYR A 147 LEU A 151 0 SHEET 2 AA2 4 LYS A 209 GLN A 214 -1 O ILE A 212 N ILE A 148 SHEET 3 AA2 4 VAL A 174 PRO A 178 -1 N PHE A 175 O GLU A 213 SHEET 4 AA2 4 SER A 188 CYS A 190 -1 O CYS A 190 N VAL A 174 SHEET 1 AA3 4 GLU A 232 ALA A 233 0 SHEET 2 AA3 4 ARG A 219 GLY A 227 -1 N LEU A 226 O GLU A 232 SHEET 3 AA3 4 GLY A 237 VAL A 239 -1 O GLY A 237 N GLU A 222 SHEET 4 AA3 4 LEU A 259 GLN A 260 -1 O GLN A 260 N GLU A 238 SHEET 1 AA4 4 GLU A 232 ALA A 233 0 SHEET 2 AA4 4 ARG A 219 GLY A 227 -1 N LEU A 226 O GLU A 232 SHEET 3 AA4 4 GLY A 288 VAL A 296 -1 O PHE A 294 N ILE A 221 SHEET 4 AA4 4 ILE A 302 ASN A 308 -1 O TYR A 303 N PHE A 295 SHEET 1 AA5 4 TRP B 49 GLN B 52 0 SHEET 2 AA5 4 HIS B 37 ILE B 43 -1 N TYR B 42 O ARG B 50 SHEET 3 AA5 4 ASN B 5 GLY B 11 1 N ILE B 8 O ILE B 41 SHEET 4 AA5 4 ALA B 90 PRO B 93 1 O PHE B 92 N CYS B 7 SHEET 1 AA6 4 TYR B 147 LEU B 151 0 SHEET 2 AA6 4 LYS B 209 GLN B 214 -1 O ILE B 212 N ILE B 148 SHEET 3 AA6 4 VAL B 174 PRO B 178 -1 N LYS B 177 O VAL B 211 SHEET 4 AA6 4 SER B 188 CYS B 190 -1 O CYS B 190 N VAL B 174 SHEET 1 AA7 4 GLU B 232 ALA B 233 0 SHEET 2 AA7 4 ARG B 219 GLY B 227 -1 N LEU B 226 O GLU B 232 SHEET 3 AA7 4 GLY B 237 VAL B 240 -1 O VAL B 239 N GLU B 220 SHEET 4 AA7 4 GLN B 258 GLN B 260 -1 O GLN B 258 N VAL B 240 SHEET 1 AA8 4 GLU B 232 ALA B 233 0 SHEET 2 AA8 4 ARG B 219 GLY B 227 -1 N LEU B 226 O GLU B 232 SHEET 3 AA8 4 GLY B 288 VAL B 296 -1 O PHE B 294 N ILE B 221 SHEET 4 AA8 4 ILE B 302 ASN B 308 -1 O ASN B 305 N ASP B 293 LINK C DAL F 1 N DAL F 2 1555 1555 1.33 LINK O ASP A 63 K K B 403 1555 1545 2.73 LINK O HIS A 66 K K B 403 1555 1545 2.80 LINK O SER A 127 K K A 401 1555 1555 2.84 LINK OE1 GLU A 306 K K A 401 1555 1555 3.03 LINK OE2 GLU A 306 MG MG A 402 1555 1555 2.13 LINK O THR A 307 K K A 401 1555 1555 2.72 LINK K K A 401 O HOH A 507 1555 1555 3.13 LINK K K A 401 O HOH A 555 1555 1555 3.14 LINK K K A 401 O HOH A 611 1555 1555 2.72 LINK K K A 401 O HOH A 654 1555 1555 2.92 LINK MG MG A 402 O1B ADP A 403 1555 1555 2.12 LINK MG MG A 402 O1A ADP A 403 1555 1555 2.07 LINK MG MG A 402 O HOH A 543 1555 1555 2.42 LINK MG MG A 402 O HOH A 586 1555 1555 2.16 LINK MG MG A 402 O HOH A 609 1555 1555 2.12 LINK O HOH A 613 K K B 403 1565 1555 2.85 LINK O SER B 127 K K B 402 1555 1555 2.93 LINK OD1 ASN B 171 K K B 403 1555 1555 3.11 LINK O TYR B 172 K K B 403 1555 1555 2.74 LINK OD2 ASP B 293 K K B 401 1555 1555 2.75 LINK OE2 GLU B 306 K K B 401 1555 1555 2.85 LINK OE1 GLU B 306 K K B 402 1555 1555 3.02 LINK OE1 GLU B 306 MG MG B 404 1555 1555 2.49 LINK OE2 GLU B 306 MG MG B 404 1555 1555 2.13 LINK O THR B 307 K K B 402 1555 1555 2.71 LINK OD1 ASN B 308 K K B 402 1555 1555 3.47 LINK OD1 ASN B 308 MG MG B 404 1555 1555 2.13 LINK K K B 401 O2A ATP B 405 1555 1555 2.68 LINK K K B 401 O3G ATP B 405 1555 1555 2.72 LINK K K B 401 O3B ATP B 405 1555 1555 3.02 LINK K K B 401 O HOH B 519 1555 1555 2.83 LINK K K B 401 O HOH B 551 1555 1555 3.32 LINK K K B 402 O HOH B 507 1555 1555 2.81 LINK K K B 402 O HOH B 535 1555 1555 3.16 LINK K K B 402 O HOH B 579 1555 1555 2.87 LINK K K B 403 O HOH B 549 1555 1555 3.39 LINK MG MG B 404 O2G ATP B 405 1555 1555 1.98 LINK MG MG B 404 O2B ATP B 405 1555 1555 2.25 LINK MG MG B 404 O HOH B 535 1555 1555 2.01 CISPEP 1 TYR A 172 PRO A 173 0 0.67 CISPEP 2 ILE A 261 PRO A 262 0 -1.69 CISPEP 3 TYR B 172 PRO B 173 0 0.19 CISPEP 4 ILE B 261 PRO B 262 0 -1.54 CRYST1 52.447 70.058 91.598 90.00 102.58 90.00 P 1 21 1 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 0.019067 0.000000 0.004256 0.00000 SCALE2 0.000000 0.014274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011186 0.00000