HEADER STRUCTURAL PROTEIN 28-APR-22 7ZPT TITLE CRYSTAL STRUCTURE OF MREB FROM GEOBACILLUS STEAROTHERMOPHILUS ATCC7953 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL SHAPE-DETERMINING PROTEIN MREB; COMPND 3 CHAIN: M; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: MREB, B4109_2230, B4114_2117, GS458_2390; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL PROTEIN, BACTERIAL ACTIN, BACTERIAL CYTOSKELETON EXPDTA X-RAY DIFFRACTION AUTHOR I.LI DE LA SIERRA-GALLAY,W.MAO REVDAT 3 07-FEB-24 7ZPT 1 REMARK REVDAT 2 25-OCT-23 7ZPT 1 JRNL REVDAT 1 10-MAY-23 7ZPT 0 JRNL AUTH W.MAO,L.D.RENNER,C.CORNILLEAU,I.LI DE LA SIERRA-GALLAY, JRNL AUTH 2 S.AFENSISS,S.BENLAMARA,Y.AH-SENG,H.VAN TILBEURGH,S.NESSLER, JRNL AUTH 3 A.BERTIN,A.CHASTANET,R.CARBALLIDO-LOPEZ JRNL TITL ON THE ROLE OF NUCLEOTIDES AND LIPIDS IN THE POLYMERIZATION JRNL TITL 2 OF THE ACTIN HOMOLOG MREB FROM A GRAM-POSITIVE BACTERIUM. JRNL REF ELIFE V. 12 2023 JRNL REFN ESSN 2050-084X JRNL PMID 37818717 JRNL DOI 10.7554/ELIFE.84505 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24968 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1249 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 46.8700 - 3.7500 1.00 2710 143 0.1658 0.1976 REMARK 3 2 3.7500 - 2.9800 1.00 2643 139 0.1863 0.2291 REMARK 3 3 2.9800 - 2.6000 1.00 2652 140 0.2092 0.2252 REMARK 3 4 2.6000 - 2.3600 1.00 2629 138 0.1936 0.2686 REMARK 3 5 2.3600 - 2.1900 1.00 2663 140 0.1938 0.2579 REMARK 3 6 2.1900 - 2.0600 1.00 2610 138 0.2062 0.2684 REMARK 3 7 2.0600 - 1.9600 1.00 2621 138 0.2099 0.2851 REMARK 3 8 1.9600 - 1.8700 1.00 2618 137 0.2399 0.3117 REMARK 3 9 1.8700 - 1.8000 0.97 2573 136 0.3050 0.3361 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.222 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.99 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 2541 REMARK 3 ANGLE : 0.965 3432 REMARK 3 CHIRALITY : 0.063 410 REMARK 3 PLANARITY : 0.011 441 REMARK 3 DIHEDRAL : 5.827 372 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 7ZPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25002 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.950 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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: MOLREP REMARK 200 STARTING MODEL: 4CZJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 300, 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID, PH 6.7, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 31.00500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: M 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 M 1 REMARK 465 PHE M 2 REMARK 465 GLY M 3 REMARK 465 ASP M 70 REMARK 465 GLY M 71 REMARK 465 VAL M 72 REMARK 465 ILE M 73 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 NH1 ARG M 124 OD1 ASP M 130 2.11 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 THR M 58 71.75 32.45 REMARK 500 PRO M 151 43.77 -79.75 REMARK 500 ARG M 181 48.11 -85.67 REMARK 500 ALA M 183 -143.56 -153.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG M 196 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF1 7ZPT M 1 340 UNP A0A150MJ77_GEOSE DBREF2 7ZPT M A0A150MJ77 1 340 SEQRES 1 M 340 MET PHE GLY ILE GLY THR LYS ASP LEU GLY ILE ASP LEU SEQRES 2 M 340 GLY THR ALA ASN THR LEU VAL TYR VAL LYS GLY LYS GLY SEQRES 3 M 340 ILE VAL LEU ARG GLU PRO SER VAL VAL ALA ILE GLN ARG SEQRES 4 M 340 ASP THR LYS GLN ILE VAL ALA VAL GLY ASN GLU ALA LYS SEQRES 5 M 340 ASN MET ILE GLY ARG THR PRO GLY ASN ILE VAL ALA LEU SEQRES 6 M 340 ARG PRO MET LYS ASP GLY VAL ILE ALA ASP TYR GLU THR SEQRES 7 M 340 THR ALA THR MET MET LYS TYR TYR ILE ARG LYS ALA ILE SEQRES 8 M 340 LYS THR LYS GLY LEU PHE ALA GLY LYS PRO TYR VAL MET SEQRES 9 M 340 VAL CYS VAL PRO TYR GLY ILE THR ALA VAL GLU GLU ARG SEQRES 10 M 340 ALA VAL ILE ASP ALA THR ARG GLN ALA GLY ALA ARG ASP SEQRES 11 M 340 ALA TYR THR ILE GLU GLU PRO PHE ALA ALA ALA ILE GLY SEQRES 12 M 340 ALA ASN LEU PRO VAL TRP GLU PRO THR GLY SER MET VAL SEQRES 13 M 340 VAL ASP ILE GLY GLY GLY THR THR GLU VAL ALA VAL ILE SEQRES 14 M 340 SER LEU GLY GLY ILE VAL THR SER GLN SER ILE ARG ILE SEQRES 15 M 340 ALA GLY ASP GLU MET ASP GLU ALA ILE ILE GLN TYR ILE SEQRES 16 M 340 ARG LYS SER TYR ASN LEU MET ILE GLY GLU ARG THR ALA SEQRES 17 M 340 GLU ALA ILE LYS MET GLU ILE GLY SER ALA GLY ASN PRO SEQRES 18 M 340 GLU GLY ILE GLY ASN MET GLU ILE ARG GLY ARG ASP LEU SEQRES 19 M 340 LEU THR GLY LEU PRO LYS THR ILE GLU ILE SER ALA GLU SEQRES 20 M 340 GLU VAL ALA GLU ALA LEU ARG ASP THR VAL TYR ALA ILE SEQRES 21 M 340 VAL GLU SER VAL LYS ASN THR LEU GLU LYS THR PRO PRO SEQRES 22 M 340 GLU LEU ALA ALA ASP ILE MET ASP ARG GLY ILE VAL LEU SEQRES 23 M 340 THR GLY GLY GLY ALA LEU LEU ARG ASN LEU ASP LYS VAL SEQRES 24 M 340 ILE SER GLN GLU THR ASP MET PRO VAL ILE VAL ALA GLU SEQRES 25 M 340 ASN PRO LEU ASP CYS VAL ALA ILE GLY THR GLY LYS ALA SEQRES 26 M 340 LEU ASP HIS ILE ASP LEU PHE LYS ASN LYS ALA ARG ASP SEQRES 27 M 340 HIS ARG HET 1PE M 401 16 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 1PE C10 H22 O6 FORMUL 3 HOH *127(H2 O) HELIX 1 AA1 GLY M 48 ARG M 57 1 10 HELIX 2 AA2 ASP M 75 ILE M 91 1 17 HELIX 3 AA3 THR M 112 ALA M 126 1 15 HELIX 4 AA4 GLU M 136 ALA M 144 1 9 HELIX 5 AA5 ALA M 183 ASN M 200 1 18 HELIX 6 AA6 GLY M 204 GLY M 216 1 13 HELIX 7 AA7 ALA M 246 LEU M 253 1 8 HELIX 8 AA8 LEU M 253 LYS M 270 1 18 HELIX 9 AA9 PRO M 272 GLY M 283 1 12 HELIX 10 AB1 GLY M 288 LEU M 293 5 6 HELIX 11 AB2 ASN M 295 ASP M 305 1 11 HELIX 12 AB3 ASP M 316 ALA M 325 1 10 HELIX 13 AB4 HIS M 328 HIS M 339 1 12 SHEET 1 AA1 5 GLY M 26 PRO M 32 0 SHEET 2 AA1 5 ASN M 17 VAL M 22 -1 N THR M 18 O GLU M 31 SHEET 3 AA1 5 LEU M 9 LEU M 13 -1 N GLY M 10 O TYR M 21 SHEET 4 AA1 5 TYR M 102 VAL M 107 1 O MET M 104 N LEU M 9 SHEET 5 AA1 5 ASP M 130 GLU M 135 1 O TYR M 132 N VAL M 105 SHEET 1 AA2 3 ILE M 44 VAL M 47 0 SHEET 2 AA2 3 VAL M 35 GLN M 38 -1 N ALA M 36 O VAL M 45 SHEET 3 AA2 3 ILE M 62 LEU M 65 -1 O LEU M 65 N VAL M 35 SHEET 1 AA3 5 GLY M 173 ILE M 180 0 SHEET 2 AA3 5 THR M 164 SER M 170 -1 N VAL M 166 O GLN M 178 SHEET 3 AA3 5 SER M 154 ILE M 159 -1 N ASP M 158 O GLU M 165 SHEET 4 AA3 5 ILE M 284 THR M 287 1 O THR M 287 N VAL M 157 SHEET 5 AA3 5 VAL M 308 VAL M 310 1 O ILE M 309 N LEU M 286 SHEET 1 AA4 3 LEU M 201 MET M 202 0 SHEET 2 AA4 3 ASN M 226 ASP M 233 -1 O ARG M 232 N MET M 202 SHEET 3 AA4 3 PRO M 239 SER M 245 -1 O ILE M 242 N ILE M 229 CRYST1 47.190 62.010 50.910 90.00 112.98 90.00 P 1 21 1 2 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 0.021191 0.000000 0.008986 0.00000 SCALE2 0.000000 0.016126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021336 0.00000 CONECT 2499 2500 CONECT 2500 2499 2501 CONECT 2501 2500 2502 CONECT 2502 2501 2504 CONECT 2503 2504 2505 CONECT 2504 2502 2503 CONECT 2505 2503 2507 CONECT 2506 2507 2508 CONECT 2507 2505 2506 CONECT 2508 2506 2510 CONECT 2509 2510 2511 CONECT 2510 2508 2509 CONECT 2511 2509 2513 CONECT 2512 2513 2514 CONECT 2513 2511 2512 CONECT 2514 2512 MASTER 249 0 1 13 16 0 0 6 2640 1 16 27 END