HEADER STRUCTURAL PROTEIN 28-APR-22 7ZPU TITLE CRYSTAL STRUCTURE OF MREB FROM GEOBACILLUS STEAROTHERMOPHILUS ATCC7953 TITLE 2 IN COMPLEX WITH ATP 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 ATCC 7953; SOURCE 3 ORGANISM_TAXID: 937593; 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 4 14-AUG-24 7ZPU 1 REMARK REVDAT 3 07-FEB-24 7ZPU 1 REMARK REVDAT 2 22-NOV-23 7ZPU 1 JRNL REVDAT 1 10-MAY-23 7ZPU 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19138 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) : 0.194 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 957 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 47.4100 - 3.7500 1.00 2668 141 0.1731 0.2339 REMARK 3 2 3.7500 - 2.9700 1.00 2610 137 0.2012 0.2350 REMARK 3 3 2.9700 - 2.6000 1.00 2620 138 0.2061 0.2399 REMARK 3 4 2.6000 - 2.3600 1.00 2599 137 0.2011 0.2373 REMARK 3 5 2.3600 - 2.1900 1.00 2573 136 0.2027 0.2894 REMARK 3 6 2.1900 - 2.0600 1.00 2597 136 0.2438 0.2822 REMARK 3 7 2.0600 - 1.9600 0.97 2514 132 0.2842 0.3432 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.575 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.98 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 2448 REMARK 3 ANGLE : 0.983 3321 REMARK 3 CHIRALITY : 0.061 398 REMARK 3 PLANARITY : 0.011 422 REMARK 3 DIHEDRAL : 6.544 345 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 7ZPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122475. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 5.5 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 : 19153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 47.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.960 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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 : 0.860 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: 7ZPT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 300, 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 30.80000 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 ILE M 4 REMARK 465 GLY M 5 REMARK 465 THR M 6 REMARK 465 ASP M 70 REMARK 465 GLY M 71 REMARK 465 VAL M 72 REMARK 465 ILE M 73 REMARK 465 THR M 93 REMARK 465 LYS M 94 REMARK 465 GLY M 95 REMARK 465 LEU M 96 REMARK 465 ASN M 334 REMARK 465 LYS M 335 REMARK 465 ALA M 336 REMARK 465 ARG M 337 REMARK 465 ASP M 338 REMARK 465 HIS M 339 REMARK 465 ARG M 340 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 76.73 55.42 REMARK 500 PRO M 151 27.71 -75.76 REMARK 500 ARG M 181 43.77 -84.32 REMARK 500 ALA M 183 -143.33 -151.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZPT RELATED DB: PDB REMARK 900 7ZPT CONTAINS THE SAME PROTEIN COMPLEXED WITH ATP REMARK 900 RELATED ID: 8AB4 RELATED DB: PDB REMARK 900 RELATED ID: 8AAM RELATED DB: PDB DBREF1 7ZPU M 1 340 UNP A0A150MJ77_GEOSE DBREF2 7ZPU 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 ATP M 401 31 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 HOH *48(H2 O) HELIX 1 AA1 GLY M 48 THR M 58 1 11 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 LYS M 333 1 6 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 THR M 164 O ILE M 180 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 ILE M 159 SHEET 5 AA3 5 VAL M 308 VAL M 310 1 O ILE M 309 N ILE M 284 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 244 N MET M 227 CRYST1 46.220 61.600 50.970 90.00 111.53 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 0.021636 0.000000 0.008536 0.00000 SCALE2 0.000000 0.016234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021091 0.00000 CONECT 2390 2391 2392 2393 2397 CONECT 2391 2390 CONECT 2392 2390 CONECT 2393 2390 CONECT 2394 2395 2396 2397 2401 CONECT 2395 2394 CONECT 2396 2394 CONECT 2397 2390 2394 CONECT 2398 2399 2400 2401 2402 CONECT 2399 2398 CONECT 2400 2398 CONECT 2401 2394 2398 CONECT 2402 2398 2403 CONECT 2403 2402 2404 CONECT 2404 2403 2405 2406 CONECT 2405 2404 2410 CONECT 2406 2404 2407 2408 CONECT 2407 2406 CONECT 2408 2406 2409 2410 CONECT 2409 2408 CONECT 2410 2405 2408 2411 CONECT 2411 2410 2412 2420 CONECT 2412 2411 2413 CONECT 2413 2412 2414 CONECT 2414 2413 2415 2420 CONECT 2415 2414 2416 2417 CONECT 2416 2415 CONECT 2417 2415 2418 CONECT 2418 2417 2419 CONECT 2419 2418 2420 CONECT 2420 2411 2414 2419 MASTER 241 0 1 13 16 0 0 6 2467 1 31 27 END