HEADER MOTOR PROTEIN 20-AUG-18 6AHP TITLE STRUCTURE OF THE 58-167 FRAGMENT OF FLIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR PROTEIN FLIL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PERIPLASMIC CORE FRAGMENT, RESIDUES 58-167; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO ALGINOLYTICUS; SOURCE 3 ORGANISM_TAXID: 663; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOLDI KEYWDS FLAGELLAR MOTOR PROTEIN, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.TAKEKAWA,M.ISUMI,M.SAKUMA,S.KOJIMA,M.HOMMA,K.IMADA REVDAT 4 03-APR-24 6AHP 1 REMARK REVDAT 3 27-MAR-24 6AHP 1 REMARK REVDAT 2 03-APR-19 6AHP 1 JRNL REVDAT 1 06-MAR-19 6AHP 0 JRNL AUTH N.TAKEKAWA,M.ISUMI,H.TERASHIMA,S.ZHU,Y.NISHINO,M.SAKUMA, JRNL AUTH 2 S.KOJIMA,M.HOMMA,K.IMADA JRNL TITL STRUCTURE OFVIBRIOFLIL, A NEW STOMATIN-LIKE PROTEIN THAT JRNL TITL 2 ASSISTS THE BACTERIAL FLAGELLAR MOTOR FUNCTION. JRNL REF MBIO V. 10 2019 JRNL REFN ESSN 2150-7511 JRNL PMID 30890608 JRNL DOI 10.1128/MBIO.00292-19 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 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 52.1010 - 4.5236 0.99 1376 147 0.1939 0.2528 REMARK 3 2 4.5236 - 3.5908 1.00 1340 147 0.1783 0.2244 REMARK 3 3 3.5908 - 3.1369 1.00 1332 149 0.1932 0.2311 REMARK 3 4 3.1369 - 2.8502 1.00 1330 144 0.2217 0.2700 REMARK 3 5 2.8502 - 2.6459 1.00 1323 142 0.2292 0.2860 REMARK 3 6 2.6459 - 2.4899 1.00 1312 150 0.2342 0.3051 REMARK 3 7 2.4899 - 2.3652 1.00 1318 147 0.2224 0.2827 REMARK 3 8 2.3652 - 2.2622 1.00 1318 148 0.2264 0.2901 REMARK 3 9 2.2622 - 2.1751 1.00 1314 145 0.2384 0.2877 REMARK 3 10 2.1751 - 2.1001 1.00 1306 149 0.2489 0.3157 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.13 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 : 0.016 1717 REMARK 3 ANGLE : 1.534 2330 REMARK 3 CHIRALITY : 0.107 278 REMARK 3 PLANARITY : 0.018 307 REMARK 3 DIHEDRAL : 12.937 1063 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 6AHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-15 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 : BL41XU 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 : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14756 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 52.101 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 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: A MODEL BUILT BY THE ROBETTA SERVER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.0, 22% (W/V) PEG REMARK 280 -4000, 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.35333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.70667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.03000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.38333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 6.67667 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 300 REMARK: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN. 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 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 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 NH2 ARG B 136 O HOH B 201 1.35 REMARK 500 OG1 THR A 78 OD1 ASP A 83 2.02 REMARK 500 CB ARG A 136 O HOH A 239 2.18 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 SER A 59 -47.09 75.82 REMARK 500 VAL A 155 -57.57 73.99 REMARK 500 VAL B 155 -54.00 67.03 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 B 84 0.28 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6AHQ RELATED DB: PDB DBREF 6AHP A 58 167 PDB 6AHP 6AHP 58 167 DBREF 6AHP B 58 167 PDB 6AHP 6AHP 58 167 SEQRES 1 A 110 ALA SER ASP ALA SER PRO ILE ALA TYR VAL ASN LEU PRO SEQRES 2 A 110 GLN ALA PHE VAL PHE ASN VAL THR GLY ASP SER ARG ASP SEQRES 3 A 110 ARG LEU VAL GLN ILE LYS ALA GLN LEU MET VAL ARG GLY SEQRES 4 A 110 ALA GLU ASN GLU GLU LEU ALA ARG TYR HIS SER PRO LEU SEQRES 5 A 110 ILE GLU SER SER LEU LEU SER THR PHE ALA SER ALA THR SEQRES 6 A 110 VAL ASP GLN LEU ARG SER PRO THR GLY ARG VAL GLU LEU SEQRES 7 A 110 ARG ASP ARG ALA SER GLU ASP ILE LYS ALA ALA LEU ASN SEQRES 8 A 110 ALA ALA VAL GLY LYS PRO VAL ILE GLU LYS VAL LEU PHE SEQRES 9 A 110 THR ASP PHE VAL ILE GLN SEQRES 1 B 110 ALA SER ASP ALA SER PRO ILE ALA TYR VAL ASN LEU PRO SEQRES 2 B 110 GLN ALA PHE VAL PHE ASN VAL THR GLY ASP SER ARG ASP SEQRES 3 B 110 ARG LEU VAL GLN ILE LYS ALA GLN LEU MET VAL ARG GLY SEQRES 4 B 110 ALA GLU ASN GLU GLU LEU ALA ARG TYR HIS SER PRO LEU SEQRES 5 B 110 ILE GLU SER SER LEU LEU SER THR PHE ALA SER ALA THR SEQRES 6 B 110 VAL ASP GLN LEU ARG SER PRO THR GLY ARG VAL GLU LEU SEQRES 7 B 110 ARG ASP ARG ALA SER GLU ASP ILE LYS ALA ALA LEU ASN SEQRES 8 B 110 ALA ALA VAL GLY LYS PRO VAL ILE GLU LYS VAL LEU PHE SEQRES 9 B 110 THR ASP PHE VAL ILE GLN FORMUL 3 HOH *159(H2 O) HELIX 1 AA1 GLY A 96 HIS A 106 1 11 HELIX 2 AA2 HIS A 106 SER A 120 1 15 HELIX 3 AA3 THR A 122 SER A 128 1 7 HELIX 4 AA4 SER A 128 GLY A 152 1 25 HELIX 5 AA5 GLY B 96 HIS B 106 1 11 HELIX 6 AA6 HIS B 106 SER B 120 1 15 HELIX 7 AA7 THR B 122 ARG B 127 1 6 HELIX 8 AA8 SER B 128 GLY B 152 1 25 SHEET 1 AA1 3 ILE A 64 THR A 78 0 SHEET 2 AA1 3 ASP A 83 ARG A 95 -1 O ILE A 88 N PHE A 73 SHEET 3 AA1 3 LYS A 158 ILE A 166 -1 O LEU A 160 N GLN A 91 SHEET 1 AA2 3 ILE B 64 ASN B 68 0 SHEET 2 AA2 3 ASP B 83 ARG B 95 -1 O VAL B 94 N ALA B 65 SHEET 3 AA2 3 PHE B 73 THR B 78 -1 N PHE B 73 O ILE B 88 SHEET 1 AA3 3 ILE B 64 ASN B 68 0 SHEET 2 AA3 3 ASP B 83 ARG B 95 -1 O VAL B 94 N ALA B 65 SHEET 3 AA3 3 LYS B 158 VAL B 165 -1 O LEU B 160 N GLN B 91 CRYST1 104.201 104.201 40.060 90.00 90.00 120.00 P 61 12 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 0.009597 0.005541 0.000000 0.00000 SCALE2 0.000000 0.011081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024962 0.00000