HEADER MOTOR PROTEIN 03-DEC-20 7DMA TITLE CRYSTAL STRUCTURE OF FLIM MIDDLE DOMAIN (46-231) WITH R49P TITLE 2 SUBSTITUTION FROM VIBRO ALGINOLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR MOTOR SWITCH PROTEIN FLIM; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 42-140; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: FLAGELLAR MOTOR SWITCH PROTEIN FLIM; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 141-231; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO ALGINOLYTICUS; SOURCE 3 ORGANISM_TAXID: 663; SOURCE 4 GENE: FLIM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: VIBRIO ALGINOLYTICUS; SOURCE 12 ORGANISM_TAXID: 663; SOURCE 13 GENE: FLIM; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS FLAGELLAR MOTOR PROTEIN, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.TAKEKAWA,M.HOMMA,K.IMADA REVDAT 3 29-NOV-23 7DMA 1 REMARK REVDAT 2 22-DEC-21 7DMA 1 JRNL REVDAT 1 07-JUL-21 7DMA 0 JRNL AUTH N.TAKEKAWA,T.NISHIKINO,T.YAMASHITA,K.HORI,Y.ONOUE,K.IHARA, JRNL AUTH 2 S.KOJIMA,M.HOMMA,K.IMADA JRNL TITL A SLIGHT BENDING OF AN ALPHA-HELIX IN FLIM CREATES A JRNL TITL 2 COUNTERCLOCKWISE-LOCKED STRUCTURE OF THE FLAGELLAR MOTOR IN JRNL TITL 3 VIBRIO. JRNL REF J.BIOCHEM. V. 170 531 2021 JRNL REFN ISSN 0021-924X JRNL PMID 34143212 JRNL DOI 10.1093/JB/MVAB074 REMARK 2 REMARK 2 RESOLUTION. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26175 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.640 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 48.4600 - 3.4800 1.00 1870 154 0.1787 0.2087 REMARK 3 2 3.4800 - 2.7600 1.00 1782 148 0.1658 0.1656 REMARK 3 3 2.7600 - 2.4100 1.00 1737 143 0.1719 0.1998 REMARK 3 4 2.4100 - 2.1900 1.00 1737 145 0.1631 0.1879 REMARK 3 5 2.1900 - 2.0300 1.00 1732 142 0.1566 0.2013 REMARK 3 6 2.0300 - 1.9100 1.00 1723 143 0.1635 0.2037 REMARK 3 7 1.9100 - 1.8200 1.00 1704 141 0.1664 0.2053 REMARK 3 8 1.8200 - 1.7400 1.00 1679 139 0.1713 0.1865 REMARK 3 9 1.7400 - 1.6700 1.00 1734 143 0.1723 0.2378 REMARK 3 10 1.6700 - 1.6100 1.00 1684 140 0.1854 0.2382 REMARK 3 11 1.6100 - 1.5600 1.00 1714 142 0.1816 0.2162 REMARK 3 12 1.5600 - 1.5200 1.00 1690 139 0.1962 0.2909 REMARK 3 13 1.5200 - 1.4800 1.00 1670 139 0.2029 0.2240 REMARK 3 14 1.4800 - 1.4400 1.00 1719 142 0.2318 0.2944 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) : 0.151 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.604 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.34 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 1663 REMARK 3 ANGLE : 1.085 2260 REMARK 3 CHIRALITY : 0.091 244 REMARK 3 PLANARITY : 0.006 301 REMARK 3 DIHEDRAL : 22.582 645 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 7DMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26243 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 75.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5X0Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % (W/V) PEG-400, 0.1 M HEPES-NAOH, REMARK 280 0.2 M NACL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.73000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.73000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.49500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 38 REMARK 465 SER A 39 REMARK 465 HIS A 40 REMARK 465 MET A 41 REMARK 465 GLN A 42 REMARK 465 ASP A 43 REMARK 465 ARG A 44 REMARK 465 ILE A 45 REMARK 465 LYS A 139 REMARK 465 ILE A 140 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 ALA B 188 67.86 -118.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 395 DISTANCE = 6.53 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7DM9 RELATED DB: PDB REMARK 900 7DM9 IS THE SAME PROTEIN WITH R49P SUBSTITUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SINGLE PROTEIN WAS DIGESTED AT THE POSITION BETWEEN A138 AND REMARK 999 E141. THE DISTANCE BETWEEN A138 AND E141 IS 30.61 ANGSTROM. REMARK 999 THEREFORE THE POLYMER HAS BEEN SPLIT IN TO TWO, CHAIN A AND CHAIN B REMARK 999 FOR CURATION. DBREF1 7DMA A 42 140 UNP A0A6F8W0A1_VIBAL DBREF2 7DMA A A0A6F8W0A1 42 140 DBREF1 7DMA B 141 231 UNP A0A6G9WZM7_VIBAL DBREF2 7DMA B A0A6G9WZM7 141 231 SEQADV 7DMA GLY A 38 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DMA SER A 39 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DMA HIS A 40 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DMA MET A 41 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DMA PRO A 49 UNP A0A6F8W0A ARG 49 ENGINEERED MUTATION SEQRES 1 A 103 GLY SER HIS MET GLN ASP ARG ILE VAL ARG GLY PRO MET SEQRES 2 A 103 PRO THR LEU GLU LEU ILE ASN GLU ARG PHE ALA ARG HIS SEQRES 3 A 103 MET ARG ILE SER LEU PHE ASN MET LEU ARG LYS THR ALA SEQRES 4 A 103 GLU VAL SER ILE ASN GLY VAL GLN MET MET LYS PHE GLY SEQRES 5 A 103 GLU TYR GLN ASN THR LEU TYR VAL PRO THR SER LEU ASN SEQRES 6 A 103 MET VAL ARG PHE ARG PRO LEU LYS GLY THR ALA LEU ILE SEQRES 7 A 103 THR MET GLU ALA ARG LEU VAL PHE ILE LEU VAL GLU ASN SEQRES 8 A 103 PHE PHE GLY GLY ASP GLY ARG PHE HIS ALA LYS ILE SEQRES 1 B 91 GLU GLY ARG GLU PHE THR PRO THR GLU ARG ARG ILE ILE SEQRES 2 B 91 GLN LEU LEU LEU LYS ILE VAL PHE GLU ASP TYR LYS GLU SEQRES 3 B 91 ALA TRP SER PRO VAL MET GLY VAL GLU PHE GLU TYR LEU SEQRES 4 B 91 ASP SER GLU VAL ASN PRO SER MET ALA ASN ILE VAL SER SEQRES 5 B 91 PRO THR GLU VAL ILE VAL VAL SER SER PHE HIS ILE GLU SEQRES 6 B 91 VAL ASP GLY GLY GLY GLY ASP PHE HIS VAL VAL MET PRO SEQRES 7 B 91 TYR SER MET VAL GLU PRO ILE ARG GLU LEU LEU ASP ALA FORMUL 3 HOH *170(H2 O) HELIX 1 AA1 MET A 50 ARG A 73 1 24 HELIX 2 AA2 PHE A 88 THR A 94 1 7 HELIX 3 AA3 ALA A 119 GLY A 132 1 14 HELIX 4 AA4 THR B 146 SER B 169 1 24 HELIX 5 AA5 ASN B 184 ALA B 188 5 5 HELIX 6 AA6 TYR B 219 GLU B 223 1 5 HELIX 7 AA7 ILE B 225 ALA B 231 1 7 SHEET 1 AA1 6 GLU A 77 LYS A 87 0 SHEET 2 AA1 6 VAL B 196 VAL B 206 -1 O ILE B 197 N MET A 86 SHEET 3 AA1 6 GLY B 209 PRO B 218 -1 O MET B 217 N VAL B 198 SHEET 4 AA1 6 ALA A 113 GLU A 118 -1 N LEU A 114 O VAL B 216 SHEET 5 AA1 6 THR A 99 ARG A 107 -1 N VAL A 104 O ALA A 113 SHEET 6 AA1 6 GLU B 175 GLU B 182 -1 O GLU B 177 N ARG A 105 CISPEP 1 VAL A 97 PRO A 98 0 -4.40 CISPEP 2 ARG A 107 PRO A 108 0 5.54 CRYST1 29.460 62.990 75.870 90.00 90.00 90.00 P 21 21 21 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 0.033944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013180 0.00000