HEADER OXIDOREDUCTASE 19-OCT-18 6MT9 TITLE X-RAY CRYSTAL STRUCTURE OF BACILLUS SUBTILIS RIBONUCLEOTIDE REDUCTASE TITLE 2 NRDE ALPHA SUBUNIT WITH TTP, ATP, AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.17.4.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: NRDE_1, B4417_3413, NCTC3610_03984; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PE-SUMO KEYWDS RIBONUCLEOTIDE REDUCTASE, ALLOSTERY, NUCLEOTIDE METABOLISM, DATP, KEYWDS 2 ATP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.C.THOMAS,F.P.BROOKS,J.P.BACIK,N.ANDO REVDAT 5 06-NOV-24 6MT9 1 REMARK REVDAT 4 11-OCT-23 6MT9 1 LINK REVDAT 3 01-JAN-20 6MT9 1 REMARK REVDAT 2 26-JUN-19 6MT9 1 JRNL REVDAT 1 19-JUN-19 6MT9 0 JRNL AUTH W.C.THOMAS,F.P.BROOKS 3RD,A.A.BURNIM,J.P.BACIK,J.STUBBE, JRNL AUTH 2 J.T.KAELBER,J.Z.CHEN,N.ANDO JRNL TITL CONVERGENT ALLOSTERY IN RIBONUCLEOTIDE REDUCTASE. JRNL REF NAT COMMUN V. 10 2653 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31201319 JRNL DOI 10.1038/S41467-019-10568-4 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 35313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2778 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 15.9987 - 6.6296 0.96 1694 152 0.1479 0.1656 REMARK 3 2 6.6296 - 5.3258 0.98 1655 143 0.1730 0.1920 REMARK 3 3 5.3258 - 4.6718 0.99 1658 138 0.1478 0.1743 REMARK 3 4 4.6718 - 4.2534 0.99 1643 142 0.1391 0.1880 REMARK 3 5 4.2534 - 3.9535 0.99 1626 138 0.1532 0.2015 REMARK 3 6 3.9535 - 3.7235 1.00 1645 140 0.1629 0.2199 REMARK 3 7 3.7235 - 3.5391 0.99 1627 141 0.1757 0.2189 REMARK 3 8 3.5391 - 3.3866 1.00 1627 139 0.1909 0.2271 REMARK 3 9 3.3866 - 3.2574 1.00 1612 139 0.1917 0.2512 REMARK 3 10 3.2574 - 3.1458 1.00 1622 140 0.2010 0.2339 REMARK 3 11 3.1458 - 3.0482 1.00 1630 135 0.2066 0.2470 REMARK 3 12 3.0482 - 2.9616 1.00 1617 139 0.2155 0.2297 REMARK 3 13 2.9616 - 2.8841 1.00 1601 141 0.1967 0.2665 REMARK 3 14 2.8841 - 2.8141 1.00 1619 134 0.2016 0.2434 REMARK 3 15 2.8141 - 2.7505 1.00 1616 134 0.1989 0.2457 REMARK 3 16 2.7505 - 2.6922 1.00 1609 134 0.2150 0.2656 REMARK 3 17 2.6922 - 2.6386 1.00 1606 140 0.2265 0.2690 REMARK 3 18 2.6386 - 2.5890 1.00 1609 134 0.2191 0.3091 REMARK 3 19 2.5890 - 2.5430 1.00 1600 140 0.2324 0.2945 REMARK 3 20 2.5430 - 2.5000 1.00 1619 135 0.2418 0.3086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5650 REMARK 3 ANGLE : 0.933 7655 REMARK 3 CHIRALITY : 0.048 829 REMARK 3 PLANARITY : 0.005 971 REMARK 3 DIHEDRAL : 20.765 2078 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 6MT9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9775 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35371 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 16.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.17500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 17.60 REMARK 200 R MERGE FOR SHELL (I) : 1.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6CGM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTAL WAS GROWN BY VAPOR REMARK 280 DIFFUSION FROM 4.5 MG/ML HOLO-NRDE IN 50 MM HEPES (PH 7.6), 50 REMARK 280 MM NACL, 5 MM MGCL2, 2 MM TCEP, AND 1% GLYCEROL, SUPPLEMENTED REMARK 280 WITH 5 MM ATP, 0.5 MM TTP, AND 1 MM GDP. THE PROTEIN SOLUTION REMARK 280 WAS INCUBATED FOR 10 MINUTES WITH FRESHLY ADDED NUCLEOTIDES REMARK 280 PRIOR TO BEING MIXED IN A 1:1 HANGING DROP WITH A PRECIPITATING REMARK 280 SOLUTION OF 6% PEG 3350, 1% W/V TRYPTONE, AND 50 MM HEPES AT PH REMARK 280 7. CRYSTALS WERE CRYOPROTECTED BY SOAKING FOR 5-10 SECONDS IN REMARK 280 WELL SOLUTION MIXED WITH 8% W/V SUCROSE, 2% W/V GLUCOSE, 8% V/V REMARK 280 GLYCEROL, 8% V/V ETHYLENE GLYCOL AND SUPPLEMENTED WITH REMARK 280 NUCLEOTIDES, TCEP, AND MGCL2 ADJUSTED TO THE SAME CONCENTRATIONS REMARK 280 USED IN THE ORIGINAL PROTEIN SOLUTIONS., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 62.71800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 63.16850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 63.16850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 94.07700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 63.16850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 63.16850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.35900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 63.16850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.16850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 94.07700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 63.16850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.16850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.35900 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 62.71800 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: 6870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 62.71800 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 SER A 2 REMARK 465 GLN A 3 REMARK 465 ASN A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 239 REMARK 465 MET A 240 REMARK 465 GLY A 241 REMARK 465 GLN A 242 REMARK 465 ARG A 243 REMARK 465 GLN A 244 REMARK 465 GLY A 245 REMARK 465 ARG A 686 REMARK 465 THR A 687 REMARK 465 LYS A 688 REMARK 465 ASP A 689 REMARK 465 THR A 690 REMARK 465 GLY A 691 REMARK 465 GLN A 692 REMARK 465 ASP A 693 REMARK 465 SER A 694 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 GLN A 19 CG CD OE1 NE2 REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 ASP A 21 CG OD1 OD2 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 HIS A 49 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 ARG A 163 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 266 CG CD CE NZ REMARK 470 ASP A 270 CG OD1 OD2 REMARK 470 ASP A 272 CG OD1 OD2 REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 LYS A 341 CG CD CE NZ REMARK 470 ASN A 608 CG OD1 ND2 REMARK 470 LYS A 610 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 LYS A 20 -103.60 -97.55 REMARK 500 TYR A 40 -65.39 -160.69 REMARK 500 ARG A 163 15.38 59.28 REMARK 500 LYS A 214 -113.61 54.64 REMARK 500 LYS A 214 -114.46 55.81 REMARK 500 SER A 593 -134.52 51.92 REMARK 500 PRO A 616 109.49 -52.00 REMARK 500 GLN A 650 -134.06 -96.29 REMARK 500 THR A 661 34.19 -87.22 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 MG A 804 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TTP A 801 O2A REMARK 620 2 TTP A 801 O1B 80.9 REMARK 620 3 TTP A 801 O3G 102.7 85.0 REMARK 620 4 HOH A 930 O 96.7 172.5 88.6 REMARK 620 5 HOH A1009 O 85.5 94.9 171.7 92.0 REMARK 620 6 HOH A1010 O 168.9 94.8 87.1 88.8 84.7 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 TTP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 804 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MVE RELATED DB: PDB REMARK 900 RELATED ID: 6MYX RELATED DB: PDB REMARK 900 RELATED ID: 6MW3 RELATED DB: PDB REMARK 900 RELATED ID: EMD-9293 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9272 RELATED DB: EMDB REMARK 900 RELATED ID: 6MV9 RELATED DB: PDB DBREF1 6MT9 A 1 700 UNP A0A162Q3J9_BACIU DBREF2 6MT9 A A0A162Q3J9 1 700 SEQRES 1 A 700 MET SER GLN ASN GLN VAL PRO LYS TRP ILE GLN LEU ASN SEQRES 2 A 700 ASN GLU ILE MET ILE GLN LYS ASP GLY LYS PHE GLN PHE SEQRES 3 A 700 ASP LYS ASP LYS GLU ALA VAL HIS SER TYR PHE VAL ASP SEQRES 4 A 700 TYR ILE ASN GLN ASN THR VAL PHE PHE HIS ASN LEU LYS SEQRES 5 A 700 GLU LYS LEU ASP TYR LEU VAL GLU ASN GLN TYR TYR GLU SEQRES 6 A 700 GLU GLU PHE LEU SER LEU TYR SER PHE GLU ASP ILE LYS SEQRES 7 A 700 GLU VAL PHE LYS THR ALA TYR ALA LYS LYS PHE ARG PHE SEQRES 8 A 700 PRO SER PHE MET SER ALA PHE LYS PHE TYR ASN ASP TYR SEQRES 9 A 700 ALA LEU LYS THR ASN ASP LYS LYS LYS ILE LEU GLU ARG SEQRES 10 A 700 TYR GLU ASP ARG ILE SER ILE VAL ALA LEU PHE PHE ALA SEQRES 11 A 700 ASN GLY ASP THR GLU LYS ALA LYS GLU TYR VAL ASN LEU SEQRES 12 A 700 MET ILE ASN GLN GLU TYR GLN PRO SER THR PRO THR PHE SEQRES 13 A 700 LEU ASN ALA GLY ARG LYS ARG ARG GLY GLU LEU VAL SER SEQRES 14 A 700 CYS PHE LEU LEU GLU VAL ASN ASP SER LEU ASN ASP ILE SEQRES 15 A 700 SER ARG ALA ILE ASP ILE SER MET GLN LEU SER LYS LEU SEQRES 16 A 700 GLY GLY GLY VAL SER LEU ASN LEU SER LYS LEU ARG ALA SEQRES 17 A 700 LYS GLY GLU ALA ILE LYS ASP VAL GLU ASN ALA THR LYS SEQRES 18 A 700 GLY VAL VAL GLY VAL MET LYS LEU LEU ASP ASN ALA PHE SEQRES 19 A 700 ARG TYR ALA ASP GLN MET GLY GLN ARG GLN GLY SER GLY SEQRES 20 A 700 ALA ALA TYR LEU ASN ILE PHE HIS ARG ASP ILE ASN ASP SEQRES 21 A 700 PHE LEU ASP THR LYS LYS ILE SER ALA ASP GLU ASP VAL SEQRES 22 A 700 ARG VAL LYS THR LEU SER ILE GLY VAL VAL ILE PRO ASP SEQRES 23 A 700 LYS PHE VAL GLU LEU ALA ARG GLU ASP LYS ALA ALA TYR SEQRES 24 A 700 VAL PHE TYR PRO HIS THR ILE TYR LYS GLU TYR GLY GLN SEQRES 25 A 700 HIS MET ASP GLU MET ASP MET ASN GLU MET TYR ASP LYS SEQRES 26 A 700 PHE VAL ASP ASN PRO ARG VAL LYS LYS GLU LYS ILE ASN SEQRES 27 A 700 PRO ARG LYS LEU LEU GLU LYS LEU ALA MET LEU ARG SER SEQRES 28 A 700 GLU SER GLY TYR PRO TYR ILE MET PHE GLN ASP ASN VAL SEQRES 29 A 700 ASN LYS VAL HIS ALA ASN ASN HIS ILE SER LYS VAL LYS SEQRES 30 A 700 PHE SER ASN LEU CYS SER GLU VAL LEU GLN ALA SER GLN SEQRES 31 A 700 VAL SER SER TYR THR ASP TYR ASP GLU GLU ASP GLU ILE SEQRES 32 A 700 GLY LEU ASP ILE SER CYS ASN LEU GLY SER LEU ASN ILE SEQRES 33 A 700 LEU ASN VAL MET GLU HIS LYS SER ILE GLU LYS THR VAL SEQRES 34 A 700 LYS LEU ALA THR ASP SER LEU THR HIS VAL SER GLU THR SEQRES 35 A 700 THR ASP ILE ARG ASN ALA PRO ALA VAL ARG ARG ALA ASN SEQRES 36 A 700 LYS ALA MET LYS SER ILE GLY LEU GLY ALA MET ASN LEU SEQRES 37 A 700 HIS GLY TYR LEU ALA GLN ASN GLY ILE ALA TYR GLU SER SEQRES 38 A 700 PRO GLU ALA ARG ASP PHE ALA ASN THR PHE PHE MET MET SEQRES 39 A 700 VAL ASN PHE TYR SER ILE GLN ARG SER ALA GLU ILE ALA SEQRES 40 A 700 LYS GLU LYS GLY GLU THR PHE ASP GLN TYR GLU GLY SER SEQRES 41 A 700 THR TYR ALA THR GLY GLU TYR PHE ASP LYS TYR VAL SER SEQRES 42 A 700 THR ASP PHE SER PRO LYS TYR GLU LYS ILE ALA ASN LEU SEQRES 43 A 700 PHE GLU GLY MET HIS ILE PRO THR THR GLU ASP TRP LYS SEQRES 44 A 700 LYS LEU LYS ALA PHE VAL ALA GLU HIS GLY MET TYR HIS SEQRES 45 A 700 SER TYR ARG LEU CYS ILE ALA PRO THR GLY SER ILE SER SEQRES 46 A 700 TYR VAL GLN SER SER THR ALA SER VAL MET PRO ILE MET SEQRES 47 A 700 GLU ARG ILE GLU GLU ARG THR TYR GLY ASN SER LYS THR SEQRES 48 A 700 TYR TYR PRO MET PRO GLY LEU ALA SER ASN ASN TRP PHE SEQRES 49 A 700 PHE TYR LYS GLU ALA TYR ASP MET ASP MET PHE LYS VAL SEQRES 50 A 700 VAL ASP MET ILE ALA THR ILE GLN GLN HIS ILE ASP GLN SEQRES 51 A 700 GLY ILE SER PHE THR LEU PHE LEU LYS ASP THR MET THR SEQRES 52 A 700 THR ARG ASP LEU ASN ARG ILE ASP LEU TYR ALA HIS HIS SEQRES 53 A 700 ARG GLY ILE LYS THR ILE TYR TYR ALA ARG THR LYS ASP SEQRES 54 A 700 THR GLY GLN ASP SER CYS LEU SER CYS VAL VAL HET TTP A 801 29 HET ADP A 802 27 HET ATP A 803 31 HET MG A 804 1 HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 TTP C10 H17 N2 O14 P3 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 MG MG 2+ FORMUL 6 HOH *194(H2 O) HELIX 1 AA1 PRO A 7 GLU A 15 1 9 HELIX 2 AA2 ILE A 16 ILE A 18 5 3 HELIX 3 AA3 ASP A 27 ASP A 39 1 13 HELIX 4 AA4 TYR A 40 THR A 45 1 6 HELIX 5 AA5 ASN A 50 ASN A 61 1 12 HELIX 6 AA6 GLU A 66 LEU A 71 1 6 HELIX 7 AA7 SER A 73 LYS A 87 1 15 HELIX 8 AA8 SER A 93 TYR A 104 1 12 HELIX 9 AA9 ARG A 117 ASN A 131 1 15 HELIX 10 AB1 ASP A 133 ASN A 146 1 14 HELIX 11 AB2 SER A 152 ALA A 159 1 8 HELIX 12 AB3 SER A 178 LEU A 195 1 18 HELIX 13 AB4 GLY A 222 ALA A 237 1 16 HELIX 14 AB5 ASP A 257 THR A 264 1 8 HELIX 15 AB6 PRO A 285 GLU A 294 1 10 HELIX 16 AB7 TYR A 302 GLY A 311 1 10 HELIX 17 AB8 HIS A 313 MET A 317 5 5 HELIX 18 AB9 ASP A 318 ASN A 329 1 12 HELIX 19 AC1 ASN A 338 GLY A 354 1 17 HELIX 20 AC2 GLN A 361 LYS A 366 1 6 HELIX 21 AC3 ILE A 416 HIS A 422 1 7 HELIX 22 AC4 SER A 424 THR A 442 1 19 HELIX 23 AC5 ALA A 448 LYS A 459 1 12 HELIX 24 AC6 ASN A 467 ASN A 475 1 9 HELIX 25 AC7 SER A 481 GLY A 511 1 31 HELIX 26 AC8 GLN A 516 GLY A 519 5 4 HELIX 27 AC9 SER A 520 GLY A 525 1 6 HELIX 28 AD1 PHE A 528 THR A 534 1 7 HELIX 29 AD2 TYR A 540 PHE A 547 1 8 HELIX 30 AD3 THR A 554 GLY A 569 1 16 HELIX 31 AD4 SER A 583 SER A 589 1 7 HELIX 32 AD5 ALA A 619 TYR A 626 5 8 HELIX 33 AD6 GLU A 628 MET A 632 5 5 HELIX 34 AD7 ASP A 633 GLN A 646 1 14 HELIX 35 AD8 THR A 663 ARG A 677 1 15 HELIX 36 AD9 CYS A 695 VAL A 699 5 5 SHEET 1 AA1 3 TYR A 149 PRO A 151 0 SHEET 2 AA1 3 LEU A 411 ASN A 415 -1 O SER A 413 N GLN A 150 SHEET 3 AA1 3 GLY A 462 MET A 466 1 O GLY A 464 N GLY A 412 SHEET 1 AA2 8 ILE A 407 SER A 408 0 SHEET 2 AA2 8 CYS A 170 GLU A 174 -1 N LEU A 172 O ILE A 407 SHEET 3 AA2 8 GLY A 198 ASN A 202 1 O SER A 200 N LEU A 173 SHEET 4 AA2 8 GLY A 247 ASN A 252 1 O ALA A 248 N LEU A 201 SHEET 5 AA2 8 LEU A 278 ILE A 284 1 O SER A 279 N GLY A 247 SHEET 6 AA2 8 TYR A 357 PHE A 360 1 O TYR A 357 N VAL A 282 SHEET 7 AA2 8 THR A 681 TYR A 684 -1 O ILE A 682 N ILE A 358 SHEET 8 AA2 8 THR A 655 LEU A 656 1 N LEU A 656 O TYR A 683 SHEET 1 AA3 2 ALA A 298 PHE A 301 0 SHEET 2 AA3 2 LYS A 334 ILE A 337 -1 O ILE A 337 N ALA A 298 SHEET 1 AA4 2 ILE A 601 TYR A 606 0 SHEET 2 AA4 2 SER A 609 PRO A 614 -1 O THR A 611 N ARG A 604 SSBOND 1 CYS A 170 CYS A 698 1555 1555 2.05 SSBOND 2 CYS A 382 CYS A 695 1555 1555 2.03 LINK O2A TTP A 801 MG MG A 804 1555 1555 1.96 LINK O1B TTP A 801 MG MG A 804 1555 1555 2.11 LINK O3G TTP A 801 MG MG A 804 1555 1555 2.16 LINK MG MG A 804 O HOH A 930 1555 1555 2.34 LINK MG MG A 804 O HOH A1009 1555 1555 2.21 LINK MG MG A 804 O HOH A1010 1555 1555 1.97 CISPEP 1 TYR A 355 PRO A 356 0 3.31 SITE 1 AC1 18 ASP A 177 SER A 178 LEU A 179 ILE A 182 SITE 2 AC1 18 LYS A 194 ARG A 207 ILE A 213 LYS A 214 SITE 3 AC1 18 THR A 220 LYS A 221 TYR A 236 ALA A 237 SITE 4 AC1 18 ASP A 238 MG A 804 HOH A 978 HOH A1008 SITE 5 AC1 18 HOH A1009 HOH A1010 SITE 1 AC2 7 VAL A 33 HIS A 34 PHE A 37 ASN A 42 SITE 2 AC2 7 ARG A 90 PHE A 91 ARG A 117 SITE 1 AC3 8 PHE A 47 PHE A 48 ASN A 50 LEU A 51 SITE 2 AC3 8 LYS A 54 LYS A 82 TYR A 85 ASP A 120 SITE 1 AC4 4 TTP A 801 HOH A 930 HOH A1009 HOH A1010 CRYST1 126.337 126.337 125.436 90.00 90.00 90.00 P 43 21 2 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 0.007915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007972 0.00000