HEADER MOTOR PROTEIN 02-DEC-20 7DM9 TITLE CRYSTAL STRUCTURE OF FLIM MIDDLE DOMAIN (51-229) FROM VIBRO TITLE 2 ALGINOLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR MOTOR SWITCH PROTEIN FLIM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE N-TERMINAL GSHM IS A REMNANT OF THE HIS-TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO ALGINOLYTICUS; SOURCE 3 ORGANISM_TAXID: 663; SOURCE 4 GENE: VAG1382_20640, VAGVIO5_20640, VAGYM19_20670, VAGYM4_20660; 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 KEYWDS FLAGELLAR MOTOR PROTEIN, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.TAKEKAWA,M.HOMMA,K.IMADA REVDAT 3 29-NOV-23 7DM9 1 REMARK REVDAT 2 22-DEC-21 7DM9 1 JRNL REVDAT 1 07-JUL-21 7DM9 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. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15438 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 : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 762 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 47.7200 - 2.9200 1.00 3084 160 0.1676 0.1775 REMARK 3 2 2.9200 - 2.3200 1.00 2917 166 0.1792 0.2285 REMARK 3 3 2.3200 - 2.0300 1.00 2940 124 0.1696 0.2173 REMARK 3 4 2.0300 - 1.8400 1.00 2859 160 0.1718 0.2402 REMARK 3 5 1.8400 - 1.7100 1.00 2876 152 0.2004 0.2591 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) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.722 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.33 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 : 0.009 1467 REMARK 3 ANGLE : 1.177 1994 REMARK 3 CHIRALITY : 0.070 223 REMARK 3 PLANARITY : 0.007 260 REMARK 3 DIHEDRAL : 24.636 559 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 7DM9 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_1300019659. 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 : 9.5 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 : 15496 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 73.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 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 (%): 19.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 % (W/V) PEG-600, 0.1 M CHES-NAOH, REMARK 280 PH 9.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 14.79000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.79000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.25000 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 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 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 VAL A 46 REMARK 465 ARG A 47 REMARK 465 GLY A 48 REMARK 465 ARG A 49 REMARK 465 MET A 50 REMARK 465 ASP A 133 REMARK 465 GLY A 134 REMARK 465 ARG A 135 REMARK 465 PHE A 136 REMARK 465 HIS A 137 REMARK 465 ALA A 138 REMARK 465 LYS A 139 REMARK 465 ILE A 140 REMARK 465 GLU A 141 REMARK 465 GLY A 142 REMARK 465 ASP A 230 REMARK 465 ALA A 231 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 ASP A 180 138.83 -171.37 REMARK 500 ALA A 188 66.87 -113.43 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7DM9 A 42 231 UNP A0A6F8W0A1_VIBAL DBREF2 7DM9 A A0A6F8W0A1 42 231 SEQADV 7DM9 GLY A 38 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DM9 SER A 39 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DM9 HIS A 40 UNP A0A6F8W0A EXPRESSION TAG SEQADV 7DM9 MET A 41 UNP A0A6F8W0A EXPRESSION TAG SEQRES 1 A 194 GLY SER HIS MET GLN ASP ARG ILE VAL ARG GLY ARG MET SEQRES 2 A 194 PRO THR LEU GLU LEU ILE ASN GLU ARG PHE ALA ARG HIS SEQRES 3 A 194 MET ARG ILE SER LEU PHE ASN MET LEU ARG LYS THR ALA SEQRES 4 A 194 GLU VAL SER ILE ASN GLY VAL GLN MET MET LYS PHE GLY SEQRES 5 A 194 GLU TYR GLN ASN THR LEU TYR VAL PRO THR SER LEU ASN SEQRES 6 A 194 MET VAL ARG PHE ARG PRO LEU LYS GLY THR ALA LEU ILE SEQRES 7 A 194 THR MET GLU ALA ARG LEU VAL PHE ILE LEU VAL GLU ASN SEQRES 8 A 194 PHE PHE GLY GLY ASP GLY ARG PHE HIS ALA LYS ILE GLU SEQRES 9 A 194 GLY ARG GLU PHE THR PRO THR GLU ARG ARG ILE ILE GLN SEQRES 10 A 194 LEU LEU LEU LYS ILE VAL PHE GLU ASP TYR LYS GLU ALA SEQRES 11 A 194 TRP SER PRO VAL MET GLY VAL GLU PHE GLU TYR LEU ASP SEQRES 12 A 194 SER GLU VAL ASN PRO SER MET ALA ASN ILE VAL SER PRO SEQRES 13 A 194 THR GLU VAL ILE VAL VAL SER SER PHE HIS ILE GLU VAL SEQRES 14 A 194 ASP GLY GLY GLY GLY ASP PHE HIS VAL VAL MET PRO TYR SEQRES 15 A 194 SER MET VAL GLU PRO ILE ARG GLU LEU LEU ASP ALA FORMUL 2 HOH *98(H2 O) HELIX 1 AA1 PRO A 51 ARG A 73 1 23 HELIX 2 AA2 PHE A 88 THR A 94 1 7 HELIX 3 AA3 ALA A 119 GLY A 131 1 13 HELIX 4 AA4 THR A 146 SER A 169 1 24 HELIX 5 AA5 ASN A 184 ALA A 188 5 5 HELIX 6 AA6 TYR A 219 GLU A 223 1 5 HELIX 7 AA7 PRO A 224 LEU A 229 5 6 SHEET 1 AA1 6 GLU A 77 LYS A 87 0 SHEET 2 AA1 6 VAL A 196 VAL A 206 -1 O HIS A 203 N SER A 79 SHEET 3 AA1 6 GLY A 209 PRO A 218 -1 O MET A 217 N VAL A 198 SHEET 4 AA1 6 ALA A 113 GLU A 118 -1 N LEU A 114 O VAL A 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 A 175 GLU A 182 -1 O ASP A 180 N MET A 103 CISPEP 1 VAL A 97 PRO A 98 0 -0.20 CISPEP 2 ARG A 107 PRO A 108 0 6.56 CRYST1 29.580 62.500 73.890 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 0.033807 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013534 0.00000