HEADER VIRUS 17-DEC-20 7DOU TITLE TRIMERIC CEMENT PROTEIN STRUCTURE OF HELICOBACTER PYLORI BACTERIOPHAGE TITLE 2 KHP40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEMENT PROTEIN GP16; COMPND 3 CHAIN: 4, 5, 6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PHAGE KHP40; SOURCE 3 ORGANISM_TAXID: 1204178 KEYWDS CAPSID, PHAGE, PHAGE HEAD, CRYOEM, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR R.KAMIYA,J.UCHIYAMA,S.MATSUZAKI,K.MURATA,K.IWASAKI,N.MIYAZAKI REVDAT 3 05-JUN-24 7DOU 1 REMARK REVDAT 2 23-FEB-22 7DOU 1 JRNL REVDAT 1 27-OCT-21 7DOU 0 JRNL AUTH R.KAMIYA,J.UCHIYAMA,S.MATSUZAKI,K.MURATA,K.IWASAKI, JRNL AUTH 2 N.MIYAZAKI JRNL TITL ACID-STABLE CAPSID STRUCTURE OF HELICOBACTER PYLORI JRNL TITL 2 BACTERIOPHAGE KHP30 BY SINGLE-PARTICLE CRYOELECTRON JRNL TITL 3 MICROSCOPY. JRNL REF STRUCTURE V. 30 300 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 34597601 JRNL DOI 10.1016/J.STR.2021.09.001 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 6772 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 7DOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019860. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HELICOBACTER PHAGE KHP 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 : 7.20 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 : FEI FALCON II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 2000.00 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 4, 5, 6 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 OE2 GLU 5 40 NZ LYS 6 79 2.16 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 THR 4 73 -0.69 67.09 REMARK 500 SER 4 85 -5.15 68.40 REMARK 500 ALA 4 98 -175.45 -66.05 REMARK 500 SER 4 101 -4.85 66.62 REMARK 500 THR 5 73 -0.66 67.10 REMARK 500 SER 5 85 -5.11 68.42 REMARK 500 ALA 5 98 -175.51 -66.01 REMARK 500 SER 5 101 -4.83 66.62 REMARK 500 THR 6 73 -0.65 67.08 REMARK 500 SER 6 85 -5.09 68.40 REMARK 500 ALA 6 98 -175.49 -66.04 REMARK 500 SER 6 101 -4.89 66.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30778 RELATED DB: EMDB REMARK 900 CAPSID STRUCTURE OF THE CLOSELY RELATED H. PYLORI PHAGE KHP30 REMARK 900 RELATED ID: EMD-30800 RELATED DB: EMDB REMARK 900 TRIMERIC CEMENT PROTEIN STRUCTURE OF HELICOBACTER PYLORI REMARK 900 BACTERIOPHAGE KHP40 DBREF 7DOU 4 1 124 UNP I7GUT5 I7GUT5_9CAUD 1 124 DBREF 7DOU 5 1 124 UNP I7GUT5 I7GUT5_9CAUD 1 124 DBREF 7DOU 6 1 124 UNP I7GUT5 I7GUT5_9CAUD 1 124 SEQRES 1 4 124 MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS SEQRES 2 4 124 ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL SEQRES 3 4 124 ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU SEQRES 4 4 124 GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL SEQRES 5 4 124 GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE SEQRES 6 4 124 LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR SEQRES 7 4 124 LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA SEQRES 8 4 124 GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG SEQRES 9 4 124 PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO SEQRES 10 4 124 SER VAL ILE GLU VAL GLU TYR SEQRES 1 5 124 MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS SEQRES 2 5 124 ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL SEQRES 3 5 124 ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU SEQRES 4 5 124 GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL SEQRES 5 5 124 GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE SEQRES 6 5 124 LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR SEQRES 7 5 124 LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA SEQRES 8 5 124 GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG SEQRES 9 5 124 PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO SEQRES 10 5 124 SER VAL ILE GLU VAL GLU TYR SEQRES 1 6 124 MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS SEQRES 2 6 124 ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL SEQRES 3 6 124 ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU SEQRES 4 6 124 GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL SEQRES 5 6 124 GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE SEQRES 6 6 124 LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR SEQRES 7 6 124 LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA SEQRES 8 6 124 GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG SEQRES 9 6 124 PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO SEQRES 10 6 124 SER VAL ILE GLU VAL GLU TYR SHEET 1 AA1 6 VAL 4 119 GLU 4 123 0 SHEET 2 AA1 6 LYS 4 2 HIS 4 6 -1 N VAL 4 5 O ILE 4 120 SHEET 3 AA1 6 SER 6 9 PHE 6 16 -1 O LEU 6 11 N HIS 4 6 SHEET 4 AA1 6 LYS 6 107 PHE 6 115 -1 O TYR 6 114 N TYR 6 10 SHEET 5 AA1 6 GLU 6 33 VAL 6 42 -1 N GLU 6 33 O PHE 6 115 SHEET 6 AA1 6 SER 6 74 VAL 6 76 -1 O GLY 6 75 N LEU 6 39 SHEET 1 AA2 6 VAL 4 119 GLU 4 123 0 SHEET 2 AA2 6 LYS 4 2 HIS 4 6 -1 N VAL 4 5 O ILE 4 120 SHEET 3 AA2 6 SER 6 9 PHE 6 16 -1 O LEU 6 11 N HIS 4 6 SHEET 4 AA2 6 LYS 6 107 PHE 6 115 -1 O TYR 6 114 N TYR 6 10 SHEET 5 AA2 6 GLU 6 33 VAL 6 42 -1 N GLU 6 33 O PHE 6 115 SHEET 6 AA2 6 TYR 6 81 THR 6 82 -1 O TYR 6 81 N VAL 6 34 SHEET 1 AA3 4 SER 4 9 PHE 4 16 0 SHEET 2 AA3 4 LYS 4 107 PHE 4 115 -1 O TYR 4 114 N TYR 4 10 SHEET 3 AA3 4 GLU 4 33 VAL 4 42 -1 N GLU 4 33 O PHE 4 115 SHEET 4 AA3 4 SER 4 74 VAL 4 76 -1 O GLY 4 75 N LEU 4 39 SHEET 1 AA4 4 SER 4 9 PHE 4 16 0 SHEET 2 AA4 4 LYS 4 107 PHE 4 115 -1 O TYR 4 114 N TYR 4 10 SHEET 3 AA4 4 GLU 4 33 VAL 4 42 -1 N GLU 4 33 O PHE 4 115 SHEET 4 AA4 4 TYR 4 81 THR 4 82 -1 O TYR 4 81 N VAL 4 34 SHEET 1 AA5 4 GLY 4 21 ALA 4 27 0 SHEET 2 AA5 4 ILE 4 88 ALA 4 96 -1 O VAL 4 93 N GLY 4 21 SHEET 3 AA5 4 GLY 4 48 LYS 4 55 -1 N LYS 4 55 O ILE 4 88 SHEET 4 AA5 4 SER 4 63 PRO 4 69 -1 O ILE 4 65 N VAL 4 52 SHEET 1 AA6 2 LYS 5 2 HIS 5 6 0 SHEET 2 AA6 2 VAL 5 119 GLU 5 123 -1 O ILE 5 120 N VAL 5 5 SHEET 1 AA7 4 SER 5 9 PHE 5 16 0 SHEET 2 AA7 4 LYS 5 107 PHE 5 115 -1 O TYR 5 114 N TYR 5 10 SHEET 3 AA7 4 GLU 5 33 VAL 5 42 -1 N GLU 5 33 O PHE 5 115 SHEET 4 AA7 4 SER 5 74 VAL 5 76 -1 O GLY 5 75 N LEU 5 39 SHEET 1 AA8 4 SER 5 9 PHE 5 16 0 SHEET 2 AA8 4 LYS 5 107 PHE 5 115 -1 O TYR 5 114 N TYR 5 10 SHEET 3 AA8 4 GLU 5 33 VAL 5 42 -1 N GLU 5 33 O PHE 5 115 SHEET 4 AA8 4 TYR 5 81 THR 5 82 -1 O TYR 5 81 N VAL 5 34 SHEET 1 AA9 4 GLY 5 21 ALA 5 27 0 SHEET 2 AA9 4 ILE 5 88 ALA 5 96 -1 O VAL 5 93 N GLY 5 21 SHEET 3 AA9 4 GLY 5 48 LYS 5 55 -1 N LYS 5 55 O ILE 5 88 SHEET 4 AA9 4 SER 5 63 PRO 5 69 -1 O ILE 5 65 N VAL 5 52 SHEET 1 AB1 2 LYS 6 2 HIS 6 6 0 SHEET 2 AB1 2 VAL 6 119 GLU 6 123 -1 O ILE 6 120 N VAL 6 5 SHEET 1 AB2 4 GLY 6 21 ALA 6 27 0 SHEET 2 AB2 4 ILE 6 88 ALA 6 96 -1 O VAL 6 93 N GLY 6 21 SHEET 3 AB2 4 GLY 6 48 LYS 6 55 -1 N LYS 6 55 O ILE 6 88 SHEET 4 AB2 4 SER 6 63 PRO 6 69 -1 O ILE 6 65 N VAL 6 52 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