HEADER CELL CYCLE 21-DEC-19 6LL6 TITLE CRSYAL STRUCTURE OF ECFTSZ (RESIDUES 11-316) 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: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FTSZ, DNQ45_06620; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS CELL DIVISION, ESCHERICHIA COLI, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR T.YOSHIZAWA,J.FUJITA,H.TERAKADA,M.OZAWA,N.KURODA,S.TANAKA,R.UEHARA, AUTHOR 2 H.MATSUMURA REVDAT 3 03-APR-24 6LL6 1 REMARK REVDAT 2 27-MAR-24 6LL6 1 REMARK REVDAT 1 26-FEB-20 6LL6 0 JRNL AUTH T.YOSHIZAWA,J.FUJITA,H.TERAKADO,M.OZAWA,N.KURODA,S.I.TANAKA, JRNL AUTH 2 R.UEHARA,H.MATSUMURA JRNL TITL CRYSTAL STRUCTURES OF THE CELL-DIVISION PROTEIN FTSZ FROM JRNL TITL 2 KLEBSIELLA PNEUMONIAE AND ESCHERICHIA COLI. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 76 86 2020 JRNL REFN ESSN 2053-230X JRNL PMID 32039890 JRNL DOI 10.1107/S2053230X2000076X 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) : 42.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8678 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 : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 433 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 42.7100 - 3.6100 1.00 2752 145 0.1638 0.2110 REMARK 3 2 3.6100 - 2.8600 1.00 2756 145 0.2059 0.2707 REMARK 3 3 2.8600 - 2.5000 1.00 2737 143 0.2132 0.2983 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.22 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 : 0.008 2216 REMARK 3 ANGLE : 1.008 3003 REMARK 3 CHIRALITY : 0.057 359 REMARK 3 PLANARITY : 0.005 396 REMARK 3 DIHEDRAL : 20.783 797 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 6LL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300015001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8681 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6400 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) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: UNRELEASED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PCB BUFFER, PEG 1500, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 GLY A 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 GLY A 63 REMARK 465 ILE A 64 REMARK 465 THR A 65 REMARK 465 LYS A 66 REMARK 465 GLY A 67 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 LYS A 170 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 ARG A 33 120.91 71.21 REMARK 500 ARG A 174 -158.85 70.81 REMARK 500 ARG A 202 55.08 -158.60 REMARK 500 ASN A 303 -66.98 -105.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 401 DBREF1 6LL6 A 11 316 UNP A0A2W6PFK5_ECOLX DBREF2 6LL6 A A0A2W6PFK5 11 316 SEQADV 6LL6 GLY A 8 UNP A0A2W6PFK EXPRESSION TAG SEQADV 6LL6 HIS A 9 UNP A0A2W6PFK EXPRESSION TAG SEQADV 6LL6 MET A 10 UNP A0A2W6PFK EXPRESSION TAG SEQRES 1 A 309 GLY HIS MET ALA VAL ILE LYS VAL ILE GLY VAL GLY GLY SEQRES 2 A 309 GLY GLY GLY ASN ALA VAL GLU HIS MET VAL ARG GLU ARG SEQRES 3 A 309 ILE GLU GLY VAL GLU PHE PHE ALA VAL ASN THR ASP ALA SEQRES 4 A 309 GLN ALA LEU ARG LYS THR ALA VAL GLY GLN THR ILE GLN SEQRES 5 A 309 ILE GLY SER GLY ILE THR LYS GLY LEU GLY ALA GLY ALA SEQRES 6 A 309 ASN PRO GLU VAL GLY ARG ASN ALA ALA ASP GLU ASP ARG SEQRES 7 A 309 ASP ALA LEU ARG ALA ALA LEU GLU GLY ALA ASP MET VAL SEQRES 8 A 309 PHE ILE ALA ALA GLY MET GLY GLY GLY THR GLY THR GLY SEQRES 9 A 309 ALA ALA PRO VAL VAL ALA GLU VAL ALA LYS ASP LEU GLY SEQRES 10 A 309 ILE LEU THR VAL ALA VAL VAL THR LYS PRO PHE ASN PHE SEQRES 11 A 309 GLU GLY LYS LYS ARG MET ALA PHE ALA GLU GLN GLY ILE SEQRES 12 A 309 THR GLU LEU SER LYS HIS VAL ASP SER LEU ILE THR ILE SEQRES 13 A 309 PRO ASN ASP LYS LEU LEU LYS VAL LEU GLY ARG GLY ILE SEQRES 14 A 309 SER LEU LEU ASP ALA PHE GLY ALA ALA ASN ASP VAL LEU SEQRES 15 A 309 LYS GLY ALA VAL GLN GLY ILE ALA GLU LEU ILE THR ARG SEQRES 16 A 309 PRO GLY LEU MET ASN VAL ASP PHE ALA ASP VAL ARG THR SEQRES 17 A 309 VAL MET SER GLU MET GLY TYR ALA MET MET GLY SER GLY SEQRES 18 A 309 VAL ALA SER GLY GLU ASP ARG ALA GLU GLU ALA ALA GLU SEQRES 19 A 309 MET ALA ILE SER SER PRO LEU LEU GLU ASP ILE ASP LEU SEQRES 20 A 309 SER GLY ALA ARG GLY VAL LEU VAL ASN ILE THR ALA GLY SEQRES 21 A 309 PHE ASP LEU ARG LEU ASP GLU PHE GLU THR VAL GLY ASN SEQRES 22 A 309 THR ILE ARG ALA PHE ALA SER ASP ASN ALA THR VAL VAL SEQRES 23 A 309 ILE GLY THR SER LEU ASP PRO ASP MET ASN ASP GLU LEU SEQRES 24 A 309 ARG VAL THR VAL VAL ALA THR GLY ILE GLY HET GDP A 401 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *10(H2 O) HELIX 1 AA1 GLY A 19 ARG A 33 1 15 HELIX 2 AA2 ASP A 45 THR A 52 1 8 HELIX 3 AA3 ASN A 73 GLU A 83 1 11 HELIX 4 AA4 ASP A 84 GLU A 93 1 10 HELIX 5 AA5 GLY A 107 LEU A 123 1 17 HELIX 6 AA6 PHE A 135 GLU A 138 5 4 HELIX 7 AA7 GLY A 139 SER A 154 1 16 HELIX 8 AA8 ASP A 166 VAL A 171 5 6 HELIX 9 AA9 SER A 177 ARG A 202 1 26 HELIX 10 AB1 ASP A 209 SER A 218 1 10 HELIX 11 AB2 ASP A 234 SER A 245 1 12 HELIX 12 AB3 SER A 246 GLU A 250 5 5 HELIX 13 AB4 ASP A 253 ALA A 257 5 5 HELIX 14 AB5 ARG A 271 ALA A 286 1 16 SHEET 1 AA110 GLN A 56 GLN A 59 0 SHEET 2 AA110 VAL A 37 ASN A 43 1 N ALA A 41 O ILE A 58 SHEET 3 AA110 ILE A 13 VAL A 18 1 N VAL A 15 O GLU A 38 SHEET 4 AA110 MET A 97 GLY A 103 1 O PHE A 99 N ILE A 16 SHEET 5 AA110 LEU A 126 LYS A 133 1 O VAL A 130 N ILE A 100 SHEET 6 AA110 SER A 159 PRO A 164 1 O ILE A 161 N ALA A 129 SHEET 7 AA110 GLY A 221 SER A 231 1 O ALA A 223 N LEU A 160 SHEET 8 AA110 GLU A 305 THR A 313 -1 O VAL A 310 N GLY A 226 SHEET 9 AA110 GLY A 259 ALA A 266 -1 N THR A 265 O ARG A 307 SHEET 10 AA110 THR A 291 LEU A 298 1 O SER A 297 N ILE A 264 SITE 1 AC1 15 GLY A 19 GLY A 20 GLY A 21 ASN A 24 SITE 2 AC1 15 GLY A 103 GLY A 106 GLY A 107 THR A 108 SITE 3 AC1 15 GLY A 109 PRO A 134 GLU A 138 PHE A 182 SITE 4 AC1 15 ASN A 186 HOH A 503 HOH A 506 CRYST1 38.280 41.670 45.030 88.79 72.06 72.45 P 1 1 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 0.026123 -0.008264 -0.009142 0.00000 SCALE2 0.000000 0.025170 0.001998 0.00000 SCALE3 0.000000 0.000000 0.023416 0.00000