HEADER LIGASE 15-AUG-19 6U1G TITLE THERMUS THERMOPHILUS D-ALANINE-D-ALANINE LIGASE IN COMPLEX WITH ATP, TITLE 2 D-ALANINE-D-ALANINE, MG2+ AND CS+ 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS (STRAIN HB8 / ATCC 27634 / SOURCE 3 DSM 579); SOURCE 4 ORGANISM_TAXID: 300852; SOURCE 5 STRAIN: HB8 / ATCC 27634 / DSM 579; SOURCE 6 GENE: DDL, TTHA1587; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ATP-GRASP DOMAIN, ATP BINDING, METAL BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.PEDERICK,J.B.BRUNING REVDAT 3 11-OCT-23 6U1G 1 LINK REVDAT 2 17-JUN-20 6U1G 1 JRNL REVDAT 1 06-MAY-20 6U1G 0 JRNL AUTH J.L.PEDERICK,A.P.THOMPSON,S.G.BELL,J.B.BRUNING JRNL TITL D-ALANINE-D-ALANINE LIGASE AS A MODEL FOR THE ACTIVATION OF JRNL TITL 2 ATP-GRASP ENZYMES BY MONOVALENT CATIONS. JRNL REF J.BIOL.CHEM. V. 295 7894 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32335509 JRNL DOI 10.1074/JBC.RA120.012936 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1750 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 47.8400 - 5.6404 1.00 2824 146 0.1751 0.1629 REMARK 3 2 5.6404 - 4.4780 1.00 2700 131 0.1444 0.1473 REMARK 3 3 4.4780 - 3.9122 1.00 2619 162 0.1455 0.1995 REMARK 3 4 3.9122 - 3.5547 1.00 2613 129 0.1726 0.2073 REMARK 3 5 3.5547 - 3.3000 1.00 2598 137 0.2082 0.2365 REMARK 3 6 3.3000 - 3.1054 1.00 2594 146 0.2229 0.2539 REMARK 3 7 3.1054 - 2.9499 1.00 2581 134 0.2461 0.3257 REMARK 3 8 2.9499 - 2.8215 1.00 2582 120 0.2496 0.3135 REMARK 3 9 2.8215 - 2.7129 1.00 2578 142 0.2495 0.3020 REMARK 3 10 2.7129 - 2.6193 1.00 2592 122 0.2525 0.2862 REMARK 3 11 2.6193 - 2.5374 1.00 2561 137 0.2714 0.3310 REMARK 3 12 2.5374 - 2.4649 1.00 2570 114 0.2904 0.3256 REMARK 3 13 2.4649 - 2.4000 1.00 2569 130 0.3093 0.4089 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.02 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 6U1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 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) : 1.4586 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.30 REMARK 200 R MERGE (I) : 0.28100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.40 REMARK 200 R MERGE FOR SHELL (I) : 3.40900 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 2.8.2 REMARK 200 STARTING MODEL: 6U1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-18% PEG 3350, 100 MM BIS-TRIS PH REMARK 280 6.8, 100 MM MAGNESIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 96.20100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.84600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.84600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.10050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.84600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.84600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 144.30150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.84600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.84600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.10050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.84600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.84600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 144.30150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 96.20100 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: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -218.0 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 HIS A 325 REMARK 465 HIS B 324 REMARK 465 HIS B 325 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 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 LYS A 138 CG CD CE NZ REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 170 CG CD OE1 NE2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 HIS A 322 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 323 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 26 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 137 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 57 140.15 -172.68 REMARK 500 LEU A 80 34.96 -98.23 REMARK 500 ASN A 205 -63.38 -99.20 REMARK 500 PHE A 207 76.44 -111.42 REMARK 500 PRO A 241 64.04 -66.20 REMARK 500 ALA A 267 145.39 -171.93 REMARK 500 PRO B 145 42.17 -80.34 REMARK 500 VAL B 206 -59.36 67.63 REMARK 500 TYR B 223 76.79 -69.00 REMARK 500 PRO B 241 85.69 -68.27 REMARK 500 ALA B 267 145.68 -171.53 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 CS A 403 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 113 O REMARK 620 2 GLU A 282 OE1 125.2 REMARK 620 3 LEU A 283 O 73.7 99.3 REMARK 620 4 ASN A 284 OD1 157.5 57.9 83.8 REMARK 620 5 HOH A 512 O 153.0 62.8 132.9 49.3 REMARK 620 6 HOH A 514 O 91.0 80.5 161.2 111.1 63.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 404 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 133 O REMARK 620 2 HOH A 578 O 83.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 270 OD2 REMARK 620 2 GLU A 282 OE2 86.9 REMARK 620 3 ATP A 407 O3G 88.2 72.3 REMARK 620 4 ATP A 407 O1A 125.6 87.1 139.8 REMARK 620 5 ATP A 407 O3B 147.8 74.1 61.5 80.1 REMARK 620 6 HOH A 549 O 88.7 149.0 77.0 119.8 94.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 282 OE1 REMARK 620 2 GLU A 282 OE2 65.3 REMARK 620 3 ASN A 284 OD1 106.4 98.4 REMARK 620 4 ATP A 407 O2G 151.2 92.7 94.6 REMARK 620 5 ATP A 407 O2B 76.8 76.1 172.0 80.0 REMARK 620 6 HOH A 512 O 111.3 172.1 89.4 87.9 96.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS B 404 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 563 O REMARK 620 2 TRP B 133 O 153.0 REMARK 620 3 HOH B 589 O 128.7 74.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS B 403 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 113 O REMARK 620 2 GLU B 282 OE1 124.2 REMARK 620 3 LEU B 283 O 72.7 97.1 REMARK 620 4 ASN B 284 OD1 157.8 55.9 85.1 REMARK 620 5 HOH B 516 O 90.6 135.3 64.6 81.1 REMARK 620 6 HOH B 519 O 148.6 64.0 138.6 53.6 102.1 REMARK 620 7 HOH B 558 O 87.4 86.6 158.1 114.2 126.0 61.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 270 OD2 REMARK 620 2 GLU B 282 OE2 100.6 REMARK 620 3 ATP B 407 O3B 152.4 74.5 REMARK 620 4 ATP B 407 O1A 136.3 80.5 70.5 REMARK 620 5 ATP B 407 O2G 95.9 75.9 56.5 125.8 REMARK 620 6 HOH B 548 O 105.0 153.4 79.4 86.1 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 282 OE1 REMARK 620 2 GLU B 282 OE2 56.0 REMARK 620 3 ASN B 284 OD1 95.8 98.0 REMARK 620 4 ATP B 407 O2B 77.5 64.1 161.7 REMARK 620 5 ATP B 407 O1G 138.8 83.6 97.8 77.5 REMARK 620 6 HOH B 519 O 117.5 162.8 98.5 99.7 98.6 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 CS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CS B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CS B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DAL A 401 and DAL A REMARK 800 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DAL B 401 and DAL B REMARK 800 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6U1C RELATED DB: PDB REMARK 900 APO FORM OF SAME PROTEIN REMARK 900 RELATED ID: 6U1D RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH DIFFERENT LIGANDS REMARK 900 RELATED ID: 6U1E RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH DIFFERENT LIGANDS REMARK 900 RELATED ID: 6U1F RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH DIFFERENT LIGANDS DBREF 6U1G A 1 319 UNP Q5SHZ3 DDL_THET8 1 319 DBREF 6U1G B 1 319 UNP Q5SHZ3 DDL_THET8 1 319 SEQADV 6U1G MET A -1 UNP Q5SHZ3 INITIATING METHIONINE SEQADV 6U1G GLU A 0 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 320 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 321 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 322 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 323 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 324 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS A 325 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G MET B -1 UNP Q5SHZ3 INITIATING METHIONINE SEQADV 6U1G GLU B 0 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 320 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 321 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 322 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 323 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 324 UNP Q5SHZ3 EXPRESSION TAG SEQADV 6U1G HIS B 325 UNP Q5SHZ3 EXPRESSION TAG SEQRES 1 A 327 MET GLU MET ARG VAL LEU LEU ILE ALA GLY GLY VAL SER SEQRES 2 A 327 PRO GLU HIS GLU VAL SER LEU LEU SER ALA GLU GLY VAL SEQRES 3 A 327 LEU ARG HIS ILE PRO PHE PRO THR ASP LEU ALA VAL ILE SEQRES 4 A 327 ALA GLN ASP GLY ARG TRP LEU LEU GLY GLU LYS ALA LEU SEQRES 5 A 327 THR ALA LEU GLU ALA LYS ALA ALA PRO GLU GLY GLU HIS SEQRES 6 A 327 PRO PHE PRO PRO PRO LEU SER TRP GLU ARG TYR ASP VAL SEQRES 7 A 327 VAL PHE PRO LEU LEU HIS GLY ARG PHE GLY GLU ASP GLY SEQRES 8 A 327 THR VAL GLN GLY PHE LEU GLU LEU LEU GLY LYS PRO TYR SEQRES 9 A 327 VAL GLY ALA GLY VAL ALA ALA SER ALA LEU CYS MET ASP SEQRES 10 A 327 LYS ASP LEU SER LYS ARG VAL LEU ALA GLN ALA GLY VAL SEQRES 11 A 327 PRO VAL VAL PRO TRP VAL ALA VAL ARG LYS GLY GLU PRO SEQRES 12 A 327 PRO VAL VAL PRO PHE ASP PRO PRO PHE PHE VAL LYS PRO SEQRES 13 A 327 ALA ASN THR GLY SER SER VAL GLY ILE SER ARG VAL GLU SEQRES 14 A 327 ARG PHE GLN ASP LEU GLU ALA ALA LEU ALA LEU ALA PHE SEQRES 15 A 327 ARG TYR ASP GLU LYS ALA VAL VAL GLU LYS ALA LEU SER SEQRES 16 A 327 PRO VAL ARG GLU LEU GLU VAL GLY VAL LEU GLY ASN VAL SEQRES 17 A 327 PHE GLY GLU ALA SER PRO VAL GLY GLU VAL ARG TYR GLU SEQRES 18 A 327 ALA PRO PHE TYR ASP TYR GLU THR LYS TYR THR PRO GLY SEQRES 19 A 327 ARG ALA GLU LEU LEU ILE PRO ALA PRO LEU ASP PRO GLY SEQRES 20 A 327 THR GLN GLU THR VAL GLN GLU LEU ALA LEU LYS ALA TYR SEQRES 21 A 327 LYS VAL LEU GLY VAL ARG GLY MET ALA ARG VAL ASP PHE SEQRES 22 A 327 PHE LEU ALA GLU GLY GLU LEU TYR LEU ASN GLU LEU ASN SEQRES 23 A 327 THR ILE PRO GLY PHE THR PRO THR SER MET TYR PRO ARG SEQRES 24 A 327 LEU PHE GLU ALA GLY GLY VAL ALA TYR PRO GLU LEU LEU SEQRES 25 A 327 ARG ARG LEU VAL GLU LEU ALA LEU THR HIS HIS HIS HIS SEQRES 26 A 327 HIS HIS SEQRES 1 B 327 MET GLU MET ARG VAL LEU LEU ILE ALA GLY GLY VAL SER SEQRES 2 B 327 PRO GLU HIS GLU VAL SER LEU LEU SER ALA GLU GLY VAL SEQRES 3 B 327 LEU ARG HIS ILE PRO PHE PRO THR ASP LEU ALA VAL ILE SEQRES 4 B 327 ALA GLN ASP GLY ARG TRP LEU LEU GLY GLU LYS ALA LEU SEQRES 5 B 327 THR ALA LEU GLU ALA LYS ALA ALA PRO GLU GLY GLU HIS SEQRES 6 B 327 PRO PHE PRO PRO PRO LEU SER TRP GLU ARG TYR ASP VAL SEQRES 7 B 327 VAL PHE PRO LEU LEU HIS GLY ARG PHE GLY GLU ASP GLY SEQRES 8 B 327 THR VAL GLN GLY PHE LEU GLU LEU LEU GLY LYS PRO TYR SEQRES 9 B 327 VAL GLY ALA GLY VAL ALA ALA SER ALA LEU CYS MET ASP SEQRES 10 B 327 LYS ASP LEU SER LYS ARG VAL LEU ALA GLN ALA GLY VAL SEQRES 11 B 327 PRO VAL VAL PRO TRP VAL ALA VAL ARG LYS GLY GLU PRO SEQRES 12 B 327 PRO VAL VAL PRO PHE ASP PRO PRO PHE PHE VAL LYS PRO SEQRES 13 B 327 ALA ASN THR GLY SER SER VAL GLY ILE SER ARG VAL GLU SEQRES 14 B 327 ARG PHE GLN ASP LEU GLU ALA ALA LEU ALA LEU ALA PHE SEQRES 15 B 327 ARG TYR ASP GLU LYS ALA VAL VAL GLU LYS ALA LEU SER SEQRES 16 B 327 PRO VAL ARG GLU LEU GLU VAL GLY VAL LEU GLY ASN VAL SEQRES 17 B 327 PHE GLY GLU ALA SER PRO VAL GLY GLU VAL ARG TYR GLU SEQRES 18 B 327 ALA PRO PHE TYR ASP TYR GLU THR LYS TYR THR PRO GLY SEQRES 19 B 327 ARG ALA GLU LEU LEU ILE PRO ALA PRO LEU ASP PRO GLY SEQRES 20 B 327 THR GLN GLU THR VAL GLN GLU LEU ALA LEU LYS ALA TYR SEQRES 21 B 327 LYS VAL LEU GLY VAL ARG GLY MET ALA ARG VAL ASP PHE SEQRES 22 B 327 PHE LEU ALA GLU GLY GLU LEU TYR LEU ASN GLU LEU ASN SEQRES 23 B 327 THR ILE PRO GLY PHE THR PRO THR SER MET TYR PRO ARG SEQRES 24 B 327 LEU PHE GLU ALA GLY GLY VAL ALA TYR PRO GLU LEU LEU SEQRES 25 B 327 ARG ARG LEU VAL GLU LEU ALA LEU THR HIS HIS HIS HIS SEQRES 26 B 327 HIS HIS HET DAL A 401 5 HET DAL A 402 6 HET CS A 403 1 HET CS A 404 1 HET MG A 405 1 HET MG A 406 1 HET ATP A 407 31 HET DAL B 401 5 HET DAL B 402 6 HET CS B 403 1 HET CS B 404 1 HET MG B 405 1 HET MG B 406 1 HET ATP B 407 31 HETNAM DAL D-ALANINE HETNAM CS CESIUM ION HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 DAL 4(C3 H7 N O2) FORMUL 5 CS 4(CS 1+) FORMUL 7 MG 4(MG 2+) FORMUL 9 ATP 2(C10 H16 N5 O13 P3) FORMUL 17 HOH *180(H2 O) HELIX 1 AA1 GLU A 13 ILE A 28 1 16 HELIX 2 AA2 GLY A 46 LYS A 56 1 11 HELIX 3 AA3 SER A 70 TYR A 74 5 5 HELIX 4 AA4 GLY A 89 GLY A 99 1 11 HELIX 5 AA5 GLY A 106 ASP A 115 1 10 HELIX 6 AA6 ASP A 117 GLY A 127 1 11 HELIX 7 AA7 ARG A 168 GLN A 170 5 3 HELIX 8 AA8 ASP A 171 PHE A 180 1 10 HELIX 9 AA9 ASP A 224 THR A 230 1 7 HELIX 10 AB1 ASP A 243 LEU A 261 1 19 HELIX 11 AB2 MET A 294 GLY A 302 1 9 HELIX 12 AB3 ALA A 305 HIS A 322 1 18 HELIX 13 AB4 GLU B 13 ILE B 28 1 16 HELIX 14 AB5 GLY B 46 LYS B 56 1 11 HELIX 15 AB6 SER B 70 TYR B 74 5 5 HELIX 16 AB7 GLY B 89 GLY B 99 1 11 HELIX 17 AB8 GLY B 106 MET B 114 1 9 HELIX 18 AB9 ASP B 115 ALA B 126 1 12 HELIX 19 AC1 ARG B 168 GLN B 170 5 3 HELIX 20 AC2 ASP B 171 PHE B 180 1 10 HELIX 21 AC3 ASP B 224 THR B 230 1 7 HELIX 22 AC4 GLY B 245 GLY B 262 1 18 HELIX 23 AC5 MET B 294 GLY B 302 1 9 HELIX 24 AC6 ALA B 305 HIS B 322 1 18 SHEET 1 AA1 4 TRP A 43 LEU A 44 0 SHEET 2 AA1 4 THR A 32 ILE A 37 -1 N VAL A 36 O LEU A 44 SHEET 3 AA1 4 VAL A 3 GLY A 8 1 N LEU A 5 O ASP A 33 SHEET 4 AA1 4 VAL A 76 PRO A 79 1 O PHE A 78 N LEU A 4 SHEET 1 AA2 4 TRP A 133 ARG A 137 0 SHEET 2 AA2 4 LYS A 185 LYS A 190 -1 O ALA A 186 N VAL A 136 SHEET 3 AA2 4 PHE A 150 PRO A 154 -1 N PHE A 151 O GLU A 189 SHEET 4 AA2 4 SER A 164 VAL A 166 -1 O SER A 164 N VAL A 152 SHEET 1 AA3 4 GLU A 209 ALA A 210 0 SHEET 2 AA3 4 ARG A 196 GLY A 204 -1 N LEU A 203 O GLU A 209 SHEET 3 AA3 4 GLY A 214 ARG A 217 -1 O GLY A 214 N GLU A 199 SHEET 4 AA3 4 GLU A 235 LEU A 237 -1 O GLU A 235 N ARG A 217 SHEET 1 AA4 4 GLU A 209 ALA A 210 0 SHEET 2 AA4 4 ARG A 196 GLY A 204 -1 N LEU A 203 O GLU A 209 SHEET 3 AA4 4 GLY A 265 ALA A 274 -1 O PHE A 271 N LEU A 198 SHEET 4 AA4 4 GLU A 277 ASN A 284 -1 O TYR A 279 N PHE A 272 SHEET 1 AA5 4 TRP B 43 LEU B 45 0 SHEET 2 AA5 4 THR B 32 ILE B 37 -1 N VAL B 36 O LEU B 44 SHEET 3 AA5 4 VAL B 3 GLY B 8 1 N LEU B 5 O ALA B 35 SHEET 4 AA5 4 VAL B 76 PRO B 79 1 O PHE B 78 N LEU B 4 SHEET 1 AA6 4 TRP B 133 ARG B 137 0 SHEET 2 AA6 4 LYS B 185 LYS B 190 -1 O ALA B 186 N VAL B 136 SHEET 3 AA6 4 PHE B 150 PRO B 154 -1 N PHE B 151 O GLU B 189 SHEET 4 AA6 4 SER B 164 VAL B 166 -1 O VAL B 166 N PHE B 150 SHEET 1 AA7 4 GLU B 209 ALA B 210 0 SHEET 2 AA7 4 ARG B 196 LEU B 203 -1 N LEU B 203 O GLU B 209 SHEET 3 AA7 4 GLY B 214 ARG B 217 -1 O GLY B 214 N GLU B 199 SHEET 4 AA7 4 GLU B 235 LEU B 237 -1 O LEU B 237 N GLU B 215 SHEET 1 AA8 4 GLU B 209 ALA B 210 0 SHEET 2 AA8 4 ARG B 196 LEU B 203 -1 N LEU B 203 O GLU B 209 SHEET 3 AA8 4 MET B 266 ALA B 274 -1 O PHE B 271 N LEU B 198 SHEET 4 AA8 4 GLU B 277 ASN B 284 -1 O TYR B 279 N PHE B 272 LINK C DAL A 401 N DAL A 402 1555 1555 1.33 LINK C DAL B 401 N DAL B 402 1555 1555 1.33 LINK O CYS A 113 CS CS A 403 1555 1555 3.06 LINK O TRP A 133 CS CS A 404 1555 1555 3.20 LINK OD2 ASP A 270 MG MG A 405 1555 1555 2.59 LINK OE1 GLU A 282 CS CS A 403 1555 1555 3.08 LINK OE2 GLU A 282 MG MG A 405 1555 1555 2.39 LINK OE1 GLU A 282 MG MG A 406 1555 1555 1.98 LINK OE2 GLU A 282 MG MG A 406 1555 1555 2.08 LINK O LEU A 283 CS CS A 403 1555 1555 3.16 LINK OD1 ASN A 284 CS CS A 403 1555 1555 3.41 LINK OD1 ASN A 284 MG MG A 406 1555 1555 1.96 LINK CS CS A 403 O HOH A 512 1555 1555 3.14 LINK CS CS A 403 O HOH A 514 1555 1555 3.35 LINK CS CS A 404 O HOH A 578 1555 1555 3.15 LINK MG MG A 405 O3G ATP A 407 1555 1555 2.42 LINK MG MG A 405 O1A ATP A 407 1555 1555 2.19 LINK MG MG A 405 O3B ATP A 407 1555 1555 2.41 LINK MG MG A 405 O HOH A 549 1555 1555 2.47 LINK MG MG A 406 O2G ATP A 407 1555 1555 1.86 LINK MG MG A 406 O2B ATP A 407 1555 1555 2.50 LINK MG MG A 406 O HOH A 512 1555 1555 1.94 LINK O HOH A 563 CS CS B 404 1555 1555 3.50 LINK O CYS B 113 CS CS B 403 1555 1555 3.01 LINK O TRP B 133 CS CS B 404 1555 1555 3.04 LINK OD2 ASP B 270 MG MG B 406 1555 1555 2.45 LINK OE1 GLU B 282 CS CS B 403 1555 1555 3.05 LINK OE1 GLU B 282 MG MG B 405 1555 1555 2.02 LINK OE2 GLU B 282 MG MG B 405 1555 1555 2.56 LINK OE2 GLU B 282 MG MG B 406 1555 1555 2.19 LINK O LEU B 283 CS CS B 403 1555 1555 3.07 LINK OD1 ASN B 284 CS CS B 403 1555 1555 3.33 LINK OD1 ASN B 284 MG MG B 405 1555 1555 2.03 LINK CS CS B 403 O HOH B 516 1555 1555 3.19 LINK CS CS B 403 O HOH B 519 1555 1555 3.22 LINK CS CS B 403 O HOH B 558 1555 1555 3.38 LINK CS CS B 404 O HOH B 589 1555 1555 3.16 LINK MG MG B 405 O2B ATP B 407 1555 1555 2.39 LINK MG MG B 405 O1G ATP B 407 1555 1555 1.91 LINK MG MG B 405 O HOH B 519 1555 1555 1.87 LINK MG MG B 406 O3B ATP B 407 1555 1555 2.86 LINK MG MG B 406 O1A ATP B 407 1555 1555 2.32 LINK MG MG B 406 O2G ATP B 407 1555 1555 2.23 LINK MG MG B 406 O HOH B 548 1555 1555 2.37 CISPEP 1 PHE A 65 PRO A 66 0 -2.91 CISPEP 2 PRO A 148 PRO A 149 0 6.28 CISPEP 3 SER A 193 PRO A 194 0 -2.65 CISPEP 4 ILE A 238 PRO A 239 0 -3.11 CISPEP 5 PHE B 65 PRO B 66 0 -5.54 CISPEP 6 PRO B 148 PRO B 149 0 2.53 CISPEP 7 SER B 193 PRO B 194 0 -2.11 CISPEP 8 ILE B 238 PRO B 239 0 -8.70 SITE 1 AC1 5 CYS A 113 GLU A 282 LEU A 283 ASN A 284 SITE 2 AC1 5 MG A 406 SITE 1 AC2 1 TRP A 133 SITE 1 AC3 4 ASP A 270 GLU A 282 ATP A 407 HOH A 549 SITE 1 AC4 5 GLU A 282 ASN A 284 CS A 403 ATP A 407 SITE 2 AC4 5 HOH A 512 SITE 1 AC5 27 LYS A 116 PHE A 151 LYS A 153 GLY A 158 SITE 2 AC5 27 SER A 159 SER A 160 ILE A 163 GLU A 189 SITE 3 AC5 27 LYS A 190 LEU A 192 GLU A 197 TYR A 218 SITE 4 AC5 27 PHE A 222 TYR A 223 LYS A 228 ARG A 268 SITE 5 AC5 27 ASP A 270 PHE A 272 ASN A 281 GLU A 282 SITE 6 AC5 27 ASN A 284 DAL A 401 DAL A 402 MG A 405 SITE 7 AC5 27 MG A 406 HOH A 512 HOH A 549 SITE 1 AC6 5 CYS B 113 GLU B 282 LEU B 283 ASN B 284 SITE 2 AC6 5 MG B 405 SITE 1 AC7 1 TRP B 133 SITE 1 AC8 5 GLU B 282 ASN B 284 CS B 403 ATP B 407 SITE 2 AC8 5 HOH B 519 SITE 1 AC9 4 ASP B 270 GLU B 282 ATP B 407 HOH B 548 SITE 1 AD1 28 LYS B 116 PHE B 151 LYS B 153 GLY B 158 SITE 2 AD1 28 SER B 159 SER B 160 ILE B 163 GLU B 189 SITE 3 AD1 28 LYS B 190 ALA B 191 LEU B 192 GLU B 197 SITE 4 AD1 28 TYR B 218 PHE B 222 TYR B 223 LYS B 228 SITE 5 AD1 28 ARG B 268 ASP B 270 PHE B 272 ASN B 281 SITE 6 AD1 28 GLU B 282 ASN B 284 DAL B 401 DAL B 402 SITE 7 AD1 28 MG B 405 MG B 406 HOH B 519 HOH B 548 SITE 1 AD2 11 GLU A 13 HIS A 82 SER A 159 LYS A 228 SITE 2 AD2 11 TYR A 229 ARG A 268 GLY A 288 SER A 293 SITE 3 AD2 11 MET A 294 ATP A 407 HOH A 509 SITE 1 AD3 12 GLU B 13 HIS B 82 LYS B 228 TYR B 229 SITE 2 AD3 12 ARG B 268 GLY B 288 SER B 293 MET B 294 SITE 3 AD3 12 ATP B 407 HOH B 521 HOH B 551 HOH B 569 CRYST1 95.692 95.692 192.402 90.00 90.00 90.00 P 41 21 2 16 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 0.010450 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005197 0.00000