HEADER CELL CYCLE 20-MAR-20 6YD5 TITLE SAFTSZ-UCM151 (COMP. 18) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION PROTEIN FTSZ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: FTSZ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL DIVISION PROTEIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR C.FERNANDEZ-TORNERO,F.M.RUIZ,J.M.ANDREU REVDAT 2 24-JAN-24 6YD5 1 REMARK REVDAT 1 28-JUL-21 6YD5 0 JRNL AUTH S.HUECAS,L.ARAUJO-BAZAN,F.M.RUIZ,L.B.RUIZ-AVILA, JRNL AUTH 2 R.F.MARTINEZ,A.ESCOBAR-PENA,M.ARTOLA,H.VAZQUEZ-VILLA, JRNL AUTH 3 M.MARTIN-FONTECHA,C.FERNANDEZ-TORNERO,M.L.LOPEZ-RODRIGUEZ, JRNL AUTH 4 J.M.ANDREU JRNL TITL TARGETING THE FTSZ ALLOSTERIC BINDING SITE WITH A NOVEL JRNL TITL 2 FLUORESCENCE POLARIZATION SCREEN, CYTOLOGICAL AND STRUCTURAL JRNL TITL 3 APPROACHES FOR ANTIBACTERIAL DISCOVERY. JRNL REF J.MED.CHEM. V. 64 5730 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33908781 JRNL DOI 10.1021/ACS.JMEDCHEM.0C02207 REMARK 2 REMARK 2 RESOLUTION. 1.55 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 41501 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2034 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 41.2200 - 3.8200 0.97 2711 160 0.1604 0.1923 REMARK 3 2 3.8200 - 3.0300 0.97 2697 141 0.1534 0.1966 REMARK 3 3 3.0300 - 2.6500 0.93 2572 125 0.1729 0.2066 REMARK 3 4 2.6500 - 2.4100 0.95 2629 115 0.1792 0.2304 REMARK 3 5 2.4100 - 2.2400 0.96 2620 151 0.2007 0.2464 REMARK 3 6 2.2400 - 2.1000 0.96 2607 124 0.2152 0.2720 REMARK 3 7 2.1000 - 2.0000 0.93 2513 123 0.2206 0.3361 REMARK 3 8 2.0000 - 1.9100 0.96 2624 125 0.2196 0.3138 REMARK 3 9 1.9100 - 1.8400 0.97 2633 139 0.2186 0.2733 REMARK 3 10 1.8400 - 1.7700 0.97 2642 148 0.2136 0.2739 REMARK 3 11 1.7700 - 1.7200 0.98 2670 122 0.2133 0.3184 REMARK 3 12 1.7200 - 1.6700 0.98 2662 147 0.2087 0.2829 REMARK 3 13 1.6700 - 1.6300 0.96 2582 156 0.2164 0.2947 REMARK 3 14 1.6300 - 1.5900 0.96 2643 127 0.2177 0.2782 REMARK 3 15 1.5900 - 1.5500 0.98 2662 131 0.2289 0.2816 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.764 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 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 2372 REMARK 3 ANGLE : 0.896 3226 REMARK 3 CHIRALITY : 0.054 378 REMARK 3 PLANARITY : 0.004 429 REMARK 3 DIHEDRAL : 18.806 895 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 6YD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-19 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97895 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 : 41526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 41.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3VOA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG5K MME, 10% ETHGLY, 0.2 M REMARK 280 LI2SO4, 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 36.20200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.09100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.20200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.09100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH12 ARG A 168 O LEU A 250 1.56 REMARK 500 OD1 ASN A 188 NH1 ARG A 191 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 303 -91.19 -115.33 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 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 200 O REMARK 620 2 VAL A 203 O 89.1 REMARK 620 3 ASN A 208 OD1 176.9 89.1 REMARK 620 4 LEU A 209 O 93.8 176.4 88.2 REMARK 620 5 OM8 A 404 O 112.6 98.2 70.2 78.8 REMARK 620 N 1 2 3 4 DBREF 6YD5 A 12 315 UNP P0A031 FTSZ_STAAU 12 315 SEQADV 6YD5 GLY A 9 UNP P0A031 EXPRESSION TAG SEQADV 6YD5 HIS A 10 UNP P0A031 EXPRESSION TAG SEQADV 6YD5 MET A 11 UNP P0A031 EXPRESSION TAG SEQRES 1 A 307 GLY HIS MET ALA THR LEU LYS VAL ILE GLY VAL GLY GLY SEQRES 2 A 307 GLY GLY ASN ASN ALA VAL ASN ARG MET ILE ASP HIS GLY SEQRES 3 A 307 MET ASN ASN VAL GLU PHE ILE ALA ILE ASN THR ASP GLY SEQRES 4 A 307 GLN ALA LEU ASN LEU SER LYS ALA GLU SER LYS ILE GLN SEQRES 5 A 307 ILE GLY GLU LYS LEU THR ARG GLY LEU GLY ALA GLY ALA SEQRES 6 A 307 ASN PRO GLU ILE GLY LYS LYS ALA ALA GLU GLU SER ARG SEQRES 7 A 307 GLU GLN ILE GLU ASP ALA ILE GLN GLY ALA ASP MET VAL SEQRES 8 A 307 PHE VAL THR SER GLY MET GLY GLY GLY THR GLY THR GLY SEQRES 9 A 307 ALA ALA PRO VAL VAL ALA LYS ILE ALA LYS GLU MET GLY SEQRES 10 A 307 ALA LEU THR VAL GLY VAL VAL THR ARG PRO PHE SER PHE SEQRES 11 A 307 GLU GLY ARG LYS ARG GLN THR GLN ALA ALA ALA GLY VAL SEQRES 12 A 307 GLU ALA MET LYS ALA ALA VAL ASP THR LEU ILE VAL ILE SEQRES 13 A 307 PRO ASN ASP ARG LEU LEU ASP ILE VAL ASP LYS SER THR SEQRES 14 A 307 PRO MET MET GLU ALA PHE LYS GLU ALA ASP ASN VAL LEU SEQRES 15 A 307 ARG GLN GLY VAL GLN GLY ILE SER ASP LEU ILE ALA VAL SEQRES 16 A 307 SER GLY GLU VAL ASN LEU ASP PHE ALA ASP VAL LYS THR SEQRES 17 A 307 ILE MET SER ASN GLN GLY SER ALA LEU MET GLY ILE GLY SEQRES 18 A 307 VAL SER SER GLY GLU ASN ARG ALA VAL GLU ALA ALA LYS SEQRES 19 A 307 LYS ALA ILE SER SER PRO LEU LEU GLU THR SER ILE VAL SEQRES 20 A 307 GLY ALA GLN GLY VAL LEU MET ASN ILE THR GLY GLY GLU SEQRES 21 A 307 SER LEU SER LEU PHE GLU ALA GLN GLU ALA ALA ASP ILE SEQRES 22 A 307 VAL GLN ASP ALA ALA ASP GLU ASP VAL ASN MET ILE PHE SEQRES 23 A 307 GLY THR VAL ILE ASN PRO GLU LEU GLN ASP GLU ILE VAL SEQRES 24 A 307 VAL THR VAL ILE ALA THR GLY PHE HET GDP A 401 38 HET MB3 A 402 16 HET K A 403 1 HET OM8 A 404 30 HET EDO A 405 10 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MB3 1-METHYLPYRROLIDIN-2-ONE HETNAM K POTASSIUM ION HETNAM OM8 3-[(3-CHLOROPHENYL)METHOXY]-2,6-BIS(FLUORANYL)BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MB3 C5 H9 N O FORMUL 4 K K 1+ FORMUL 5 OM8 C14 H10 CL F2 N O2 FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *225(H2 O) HELIX 1 AA1 GLY A 20 HIS A 33 1 14 HELIX 2 AA2 ASP A 46 LEU A 52 1 7 HELIX 3 AA3 GLY A 62 ARG A 67 1 6 HELIX 4 AA4 ASN A 74 SER A 85 1 12 HELIX 5 AA5 SER A 85 GLN A 94 1 10 HELIX 6 AA6 GLY A 108 MET A 124 1 17 HELIX 7 AA7 PHE A 136 GLU A 139 5 4 HELIX 8 AA8 GLY A 140 ALA A 156 1 17 HELIX 9 AA9 ASP A 167 ILE A 172 5 6 HELIX 10 AB1 PRO A 178 VAL A 203 1 26 HELIX 11 AB2 ASP A 210 SER A 219 1 10 HELIX 12 AB3 ASN A 235 SER A 246 1 12 HELIX 13 AB4 SER A 271 ASP A 284 1 14 SHEET 1 AA110 SER A 57 GLN A 60 0 SHEET 2 AA110 VAL A 38 ASN A 44 1 N ALA A 42 O ILE A 59 SHEET 3 AA110 LEU A 14 VAL A 19 1 N VAL A 16 O GLU A 39 SHEET 4 AA110 MET A 98 GLY A 104 1 O PHE A 100 N ILE A 17 SHEET 5 AA110 LEU A 127 ARG A 134 1 O LEU A 127 N VAL A 99 SHEET 6 AA110 THR A 160 PRO A 165 1 O ILE A 164 N VAL A 132 SHEET 7 AA110 GLY A 222 SER A 231 1 O GLY A 222 N LEU A 161 SHEET 8 AA110 ILE A 306 THR A 313 -1 O VAL A 308 N GLY A 229 SHEET 9 AA110 GLY A 259 GLY A 266 -1 N LEU A 261 O ILE A 311 SHEET 10 AA110 ASN A 291 ILE A 298 1 O ASN A 291 N VAL A 260 LINK O LEU A 200 K K A 403 1555 1555 2.58 LINK O VAL A 203 K K A 403 1555 1555 2.42 LINK OD1 ASN A 208 K K A 403 1555 1555 2.64 LINK O LEU A 209 K K A 403 1555 1555 2.61 LINK K K A 403 O OM8 A 404 1555 1555 2.60 CRYST1 72.404 50.182 88.600 90.00 111.49 90.00 C 1 2 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 0.013811 0.000000 0.005438 0.00000 SCALE2 0.000000 0.019927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012130 0.00000