HEADER STRUCTURAL PROTEIN 09-FEB-22 7TXI TITLE CRYO-EM OF A. PERNIX FLAGELLUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE FLAGELLIN 1; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636 KEYWDS HELICAL SYMMETRY, FLAGELLUM, CELL APPENDAGE, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.WANG,V.CVIRKAITE-KRUPOVIC,D.P.BAQUERO,M.KRUPOVIC,E.H.EGELMAN REVDAT 2 16-AUG-23 7TXI 1 JRNL REVDAT 1 01-JUN-22 7TXI 0 JRNL AUTH M.A.B.KREUTZBERGER,V.CVIRKAITE-KRUPOVIC,Y.LIU,D.P.BAQUERO, JRNL AUTH 2 J.LIU,R.R.SONANI,C.R.CALLADINE,F.WANG,M.KRUPOVIC,E.H.EGELMAN JRNL TITL THE EVOLUTION OF ARCHAEAL FLAGELLAR FILAMENTS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 56120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37399404 JRNL DOI 10.1073/PNAS.2304256120 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.500 REMARK 3 NUMBER OF PARTICLES : 59338 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7TXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000263087. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : A. PERNIX FLAGELLUM REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 108.00 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 5.52 ANGSTROMS 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 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 -55.16000 REMARK 350 BIOMT1 2 -0.309017 -0.951057 0.000000 0.00000 REMARK 350 BIOMT2 2 0.951057 -0.309017 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -49.64400 REMARK 350 BIOMT1 3 -0.809017 0.587785 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.587785 -0.809017 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -44.12800 REMARK 350 BIOMT1 4 0.809017 0.587785 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.587785 0.809017 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -38.61200 REMARK 350 BIOMT1 5 0.309017 -0.951057 0.000000 0.00000 REMARK 350 BIOMT2 5 0.951057 0.309017 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -33.09600 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -27.58000 REMARK 350 BIOMT1 7 0.309017 0.951057 0.000000 0.00000 REMARK 350 BIOMT2 7 -0.951057 0.309017 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -22.06400 REMARK 350 BIOMT1 8 0.809017 -0.587785 0.000000 0.00000 REMARK 350 BIOMT2 8 0.587785 0.809017 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -16.54800 REMARK 350 BIOMT1 9 -0.809017 -0.587785 0.000000 0.00000 REMARK 350 BIOMT2 9 0.587785 -0.809017 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -11.03200 REMARK 350 BIOMT1 10 -0.309017 0.951057 0.000000 0.00000 REMARK 350 BIOMT2 10 -0.951057 -0.309017 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -5.51600 REMARK 350 BIOMT1 11 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 -0.309017 -0.951057 0.000000 0.00000 REMARK 350 BIOMT2 12 0.951057 -0.309017 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 5.51600 REMARK 350 BIOMT1 13 -0.809017 0.587785 0.000000 0.00000 REMARK 350 BIOMT2 13 -0.587785 -0.809017 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 11.03200 REMARK 350 BIOMT1 14 0.809017 0.587785 0.000000 0.00000 REMARK 350 BIOMT2 14 -0.587785 0.809017 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 16.54800 REMARK 350 BIOMT1 15 0.309017 -0.951057 0.000000 0.00000 REMARK 350 BIOMT2 15 0.951057 0.309017 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 22.06400 REMARK 350 BIOMT1 16 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 27.58000 REMARK 350 BIOMT1 17 0.309017 0.951057 0.000000 0.00000 REMARK 350 BIOMT2 17 -0.951057 0.309017 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 33.09600 REMARK 350 BIOMT1 18 0.809017 -0.587785 0.000000 0.00000 REMARK 350 BIOMT2 18 0.587785 0.809017 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 38.61200 REMARK 350 BIOMT1 19 -0.809017 -0.587785 0.000000 0.00000 REMARK 350 BIOMT2 19 0.587785 -0.809017 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 44.12800 REMARK 350 BIOMT1 20 -0.309017 0.951057 0.000000 0.00000 REMARK 350 BIOMT2 20 -0.951057 -0.309017 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 49.64400 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 A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 ILE A 7 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 165 CG PRO A 165 CD -0.228 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 165 C - N - CD ANGL. DEV. = -20.4 DEGREES REMARK 500 PRO A 165 CA - N - CD ANGL. DEV. = -13.5 DEGREES REMARK 500 PRO A 165 N - CD - CG ANGL. DEV. = -12.4 DEGREES 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 54 63.19 62.34 REMARK 500 LEU A 56 132.04 70.91 REMARK 500 ARG A 84 -129.59 51.97 REMARK 500 SER A 117 -5.64 73.19 REMARK 500 LEU A 118 -140.51 53.12 REMARK 500 SER A 121 32.09 -98.44 REMARK 500 LEU A 166 71.82 64.81 REMARK 500 ASN A 167 -160.66 -75.28 REMARK 500 TYR A 169 -4.91 76.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26158 RELATED DB: EMDB REMARK 900 CRYO-EM OF A. PERNIX FLAGELLUM DBREF 7TXI A 1 203 UNP Q9YAN8 FLAB1_AERPE 1 203 SEQRES 1 A 203 MET ARG ARG ARG ARG GLY ILE VAL GLY ILE GLU ALA ALA SEQRES 2 A 203 ILE VAL LEU ILE ALA PHE VAL ILE VAL ALA ALA ALA LEU SEQRES 3 A 203 ALA PHE VAL ALA LEU ASN MET GLY LEU PHE THR THR GLN SEQRES 4 A 203 LYS SER LYS GLU VAL MET GLN ARG GLY LEU GLU GLU ALA SEQRES 5 A 203 THR SER ALA LEU GLU VAL ASP GLY SER VAL ILE ALA ASN SEQRES 6 A 203 VAL THR SER GLY SER VAL ASP ALA ILE ALA ILE PRO ILE SEQRES 7 A 203 LYS VAL SER PRO GLY ARG GLU GLY VAL ASP MET SER VAL SEQRES 8 A 203 ASP LYS THR THR VAL ARG VAL MET LEU PRO SER LYS PHE SEQRES 9 A 203 TYR GLU ASN ALA TYR CYS GLY VAL PHE ASP GLY SER SER SEQRES 10 A 203 LEU SER ASP SER LYS LEU SER THR ILE THR SER SER ILE SEQRES 11 A 203 ALA CYS THR THR GLY TRP ALA TYR LEU VAL ILE PHE ASN SEQRES 12 A 203 GLY ASP GLY ASP ASN VAL LEU GLU LEU GLY GLU LYS GLY SEQRES 13 A 203 LEU LEU VAL LEU GLU LEU PRO THR PRO LEU ASN SER TYR SEQRES 14 A 203 GLU GLU PHE LYS VAL GLU VAL ARG PRO VAL GLN GLY ALA SEQRES 15 A 203 ALA LEU THR VAL GLU ARG ILE VAL PRO ALA SER LEU PRO SEQRES 16 A 203 THR GLY GLY ALA VAL SER LEU GLY HELIX 1 AA1 VAL A 8 THR A 53 1 46 HELIX 2 AA2 LYS A 122 ILE A 130 1 9 SHEET 1 AA1 5 GLU A 57 VAL A 58 0 SHEET 2 AA1 5 SER A 70 LYS A 79 -1 O LYS A 79 N GLU A 57 SHEET 3 AA1 5 LYS A 155 GLU A 161 -1 O LEU A 158 N ILE A 76 SHEET 4 AA1 5 ALA A 137 PHE A 142 -1 N PHE A 142 O LYS A 155 SHEET 5 AA1 5 TYR A 109 ASP A 114 1 N CYS A 110 O ALA A 137 SHEET 1 AA2 4 GLU A 57 VAL A 58 0 SHEET 2 AA2 4 SER A 70 LYS A 79 -1 O LYS A 79 N GLU A 57 SHEET 3 AA2 4 ILE A 63 THR A 67 -1 N ASN A 65 O ASP A 72 SHEET 4 AA2 4 ALA A 199 SER A 201 -1 O VAL A 200 N ALA A 64 SHEET 1 AA3 2 VAL A 87 ASP A 88 0 SHEET 2 AA3 2 VAL A 149 LEU A 150 -1 O LEU A 150 N VAL A 87 SHEET 1 AA4 4 PHE A 104 TYR A 105 0 SHEET 2 AA4 4 THR A 95 MET A 99 -1 N VAL A 98 O TYR A 105 SHEET 3 AA4 4 GLU A 171 ARG A 177 -1 O LYS A 173 N MET A 99 SHEET 4 AA4 4 LEU A 184 ILE A 189 -1 O VAL A 186 N VAL A 174 SSBOND 1 CYS A 110 CYS A 132 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000