HEADER STRUCTURAL PROTEIN 19-MAY-03 1PDJ TITLE FITTING OF GP27 INTO CRYOEM RECONSTRUCTION OF BACTERIOPHAGE T4 TITLE 2 BASEPLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASEPLATE STRUCTURAL PROTEIN GP27; COMPND 3 CHAIN: D, E, F; COMPND 4 SYNONYM: HUB PROTEIN 27 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665 KEYWDS STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN D, E, F AUTHOR V.A.KOSTYUCHENKO,P.G.LEIMAN,P.R.CHIPMAN,S.KANAMARU,M.J.VAN RAAIJ, AUTHOR 2 F.ARISAKA,V.V.MESYANZHINOV,M.G.ROSSMANN REVDAT 4 14-FEB-24 1PDJ 1 REMARK REVDAT 3 18-JUL-18 1PDJ 1 REMARK REVDAT 2 24-FEB-09 1PDJ 1 VERSN REVDAT 1 09-SEP-03 1PDJ 0 JRNL AUTH V.A.KOSTYUCHENKO,P.G.LEIMAN,P.R.CHIPMAN,S.KANAMARU, JRNL AUTH 2 M.J.VAN RAAIJ,F.ARISAKA,V.V.MESYANZHINOV,M.G.ROSSMANN JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE BACTERIOPHAGE T4 JRNL TITL 2 BASEPLATE JRNL REF NAT.STRUCT.BIOL. V. 10 688 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12923574 JRNL DOI 10.1038/NSB970 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.KANAMARU,P.G.LEIMAN,V.A.KOSTYUCHENKO,P.R.CHIPMAN, REMARK 1 AUTH 2 V.V.MESYANZHINOV,F.ARISAKA,M.G.ROSSMANN REMARK 1 TITL STRUCTURE OF THE CELL-PUNCTURING DEVICE OF BACTERIOPHAGE T4 REMARK 1 REF NATURE V. 415 553 2002 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 12.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SITUS COLORES, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1K28 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 MAXIMIZATION REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--LAPLACIAN FILTERED REAL REMARK 3 SPACE REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 3.110 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.00 REMARK 3 NUMBER OF PARTICLES : 945 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV IMAGES REMARK 3 REMARK 3 OTHER DETAILS: A MODIFIED VERSION OF SPIDER WAS USED FOR THE REMARK 3 RECONSTRUCTION REMARK 4 REMARK 4 1PDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019252. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : T4 BASEPLATE-TAIL TUBE COMPLEX; REMARK 245 GP27 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : ETHANE VITRIFICATION REMARK 245 SAMPLE BUFFER : WATER REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : TRIMER REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 30-JAN-01 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 70.00 REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM300FEG/T REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : 47000 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 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY REMARK 300 SIGNIFICANT MULTIMER. REMARK 300 ASSEMBLY COMPONENTS REMARK 300 COM_ID: 1 REMARK 300 NAME:GP27 REMARK 300 IPR_ID: NULL REMARK 300 GO_ID: NULL REMARK 300 OTHER_DETAILS: TRIMER 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: D, E, F 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 MET D 1 REMARK 465 SER D 2 REMARK 465 MET D 3 REMARK 465 LEU D 218 REMARK 465 ILE D 219 REMARK 465 GLY D 220 REMARK 465 GLN D 221 REMARK 465 PHE D 222 REMARK 465 ILE D 223 REMARK 465 GLN D 224 REMARK 465 GLU D 225 REMARK 465 LEU D 226 REMARK 465 LYS D 377 REMARK 465 SER D 378 REMARK 465 ASP D 379 REMARK 465 THR D 380 REMARK 465 THR D 381 REMARK 465 THR D 382 REMARK 465 GLU D 383 REMARK 465 GLU D 384 REMARK 465 SER D 385 REMARK 465 SER D 386 REMARK 465 SER D 387 REMARK 465 SER D 388 REMARK 465 ASN D 389 REMARK 465 LYS D 390 REMARK 465 GLN D 391 REMARK 465 MET E 1 REMARK 465 SER E 2 REMARK 465 MET E 3 REMARK 465 LEU E 218 REMARK 465 ILE E 219 REMARK 465 GLY E 220 REMARK 465 GLN E 221 REMARK 465 PHE E 222 REMARK 465 ILE E 223 REMARK 465 GLN E 224 REMARK 465 GLU E 225 REMARK 465 LEU E 226 REMARK 465 LYS E 377 REMARK 465 SER E 378 REMARK 465 ASP E 379 REMARK 465 THR E 380 REMARK 465 THR E 381 REMARK 465 THR E 382 REMARK 465 GLU E 383 REMARK 465 GLU E 384 REMARK 465 SER E 385 REMARK 465 SER E 386 REMARK 465 SER E 387 REMARK 465 SER E 388 REMARK 465 ASN E 389 REMARK 465 LYS E 390 REMARK 465 GLN E 391 REMARK 465 MET F 1 REMARK 465 SER F 2 REMARK 465 MET F 3 REMARK 465 LEU F 218 REMARK 465 ILE F 219 REMARK 465 GLY F 220 REMARK 465 GLN F 221 REMARK 465 PHE F 222 REMARK 465 ILE F 223 REMARK 465 GLN F 224 REMARK 465 GLU F 225 REMARK 465 LEU F 226 REMARK 465 LYS F 377 REMARK 465 SER F 378 REMARK 465 ASP F 379 REMARK 465 THR F 380 REMARK 465 THR F 381 REMARK 465 THR F 382 REMARK 465 GLU F 383 REMARK 465 GLU F 384 REMARK 465 SER F 385 REMARK 465 SER F 386 REMARK 465 SER F 387 REMARK 465 SER F 388 REMARK 465 ASN F 389 REMARK 465 LYS F 390 REMARK 465 GLN F 391 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K28 RELATED DB: PDB REMARK 900 GP27 IS A PART OF THE CELL-PUNCTURING DEVICE, PART OF THE BASEPLATE REMARK 900 RELATED ID: EMD-1048 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ONLY COORDINTES FOR CA ATOMS SUBMITTED. DBREF 1PDJ D 1 391 UNP P17172 VG27_BPT4 1 391 DBREF 1PDJ E 1 391 UNP P17172 VG27_BPT4 1 391 DBREF 1PDJ F 1 391 UNP P17172 VG27_BPT4 1 391 SEQRES 1 D 391 MET SER MET LEU GLN ARG PRO GLY TYR PRO ASN LEU SER SEQRES 2 D 391 VAL LYS LEU PHE ASP SER TYR ASP ALA TRP SER ASN ASN SEQRES 3 D 391 ARG PHE VAL GLU LEU ALA ALA THR ILE THR THR LEU THR SEQRES 4 D 391 MET ARG ASP SER LEU TYR GLY ARG ASN GLU GLY MET LEU SEQRES 5 D 391 GLN PHE TYR ASP SER LYS ASN ILE HIS THR LYS MET ASP SEQRES 6 D 391 GLY ASN GLU ILE ILE GLN ILE SER VAL ALA ASN ALA ASN SEQRES 7 D 391 ASP ILE ASN ASN VAL LYS THR ARG ILE TYR GLY CYS LYS SEQRES 8 D 391 HIS PHE SER VAL SER VAL ASP SER LYS GLY ASP ASN ILE SEQRES 9 D 391 ILE ALA ILE GLU LEU GLY THR ILE HIS SER ILE GLU ASN SEQRES 10 D 391 LEU LYS PHE GLY ARG PRO PHE PHE PRO ASP ALA GLY GLU SEQRES 11 D 391 SER ILE LYS GLU MET LEU GLY VAL ILE TYR GLN ASP ARG SEQRES 12 D 391 THR LEU LEU THR PRO ALA ILE ASN ALA ILE ASN ALA TYR SEQRES 13 D 391 VAL PRO ASP ILE PRO TRP THR SER THR PHE GLU ASN TYR SEQRES 14 D 391 LEU SER TYR VAL ARG GLU VAL ALA LEU ALA VAL GLY SER SEQRES 15 D 391 ASP LYS PHE VAL PHE VAL TRP GLN ASP ILE MET GLY VAL SEQRES 16 D 391 ASN MET MET ASP TYR ASP MET MET ILE ASN GLN GLU PRO SEQRES 17 D 391 TYR PRO MET ILE VAL GLY GLU PRO SER LEU ILE GLY GLN SEQRES 18 D 391 PHE ILE GLN GLU LEU LYS TYR PRO LEU ALA TYR ASP PHE SEQRES 19 D 391 VAL TRP LEU THR LYS SER ASN PRO HIS LYS ARG ASP PRO SEQRES 20 D 391 MET LYS ASN ALA THR ILE TYR ALA HIS SER PHE LEU ASP SEQRES 21 D 391 SER SER ILE PRO MET ILE THR THR GLY LYS GLY GLU ASN SEQRES 22 D 391 SER ILE VAL VAL SER ARG SER GLY ALA TYR SER GLU MET SEQRES 23 D 391 THR TYR ARG ASN GLY TYR GLU GLU ALA ILE ARG LEU GLN SEQRES 24 D 391 THR MET ALA GLN TYR ASP GLY TYR ALA LYS CYS SER THR SEQRES 25 D 391 ILE GLY ASN PHE ASN LEU THR PRO GLY VAL LYS ILE ILE SEQRES 26 D 391 PHE ASN ASP SER LYS ASN GLN PHE LYS THR GLU PHE TYR SEQRES 27 D 391 VAL ASP GLU VAL ILE HIS GLU LEU SER ASN ASN ASN SER SEQRES 28 D 391 VAL THR HIS LEU TYR MET PHE THR ASN ALA THR LYS LEU SEQRES 29 D 391 GLU THR ILE ASP PRO VAL LYS VAL LYS ASN GLU PHE LYS SEQRES 30 D 391 SER ASP THR THR THR GLU GLU SER SER SER SER ASN LYS SEQRES 31 D 391 GLN SEQRES 1 E 391 MET SER MET LEU GLN ARG PRO GLY TYR PRO ASN LEU SER SEQRES 2 E 391 VAL LYS LEU PHE ASP SER TYR ASP ALA TRP SER ASN ASN SEQRES 3 E 391 ARG PHE VAL GLU LEU ALA ALA THR ILE THR THR LEU THR SEQRES 4 E 391 MET ARG ASP SER LEU TYR GLY ARG ASN GLU GLY MET LEU SEQRES 5 E 391 GLN PHE TYR ASP SER LYS ASN ILE HIS THR LYS MET ASP SEQRES 6 E 391 GLY ASN GLU ILE ILE GLN ILE SER VAL ALA ASN ALA ASN SEQRES 7 E 391 ASP ILE ASN ASN VAL LYS THR ARG ILE TYR GLY CYS LYS SEQRES 8 E 391 HIS PHE SER VAL SER VAL ASP SER LYS GLY ASP ASN ILE SEQRES 9 E 391 ILE ALA ILE GLU LEU GLY THR ILE HIS SER ILE GLU ASN SEQRES 10 E 391 LEU LYS PHE GLY ARG PRO PHE PHE PRO ASP ALA GLY GLU SEQRES 11 E 391 SER ILE LYS GLU MET LEU GLY VAL ILE TYR GLN ASP ARG SEQRES 12 E 391 THR LEU LEU THR PRO ALA ILE ASN ALA ILE ASN ALA TYR SEQRES 13 E 391 VAL PRO ASP ILE PRO TRP THR SER THR PHE GLU ASN TYR SEQRES 14 E 391 LEU SER TYR VAL ARG GLU VAL ALA LEU ALA VAL GLY SER SEQRES 15 E 391 ASP LYS PHE VAL PHE VAL TRP GLN ASP ILE MET GLY VAL SEQRES 16 E 391 ASN MET MET ASP TYR ASP MET MET ILE ASN GLN GLU PRO SEQRES 17 E 391 TYR PRO MET ILE VAL GLY GLU PRO SER LEU ILE GLY GLN SEQRES 18 E 391 PHE ILE GLN GLU LEU LYS TYR PRO LEU ALA TYR ASP PHE SEQRES 19 E 391 VAL TRP LEU THR LYS SER ASN PRO HIS LYS ARG ASP PRO SEQRES 20 E 391 MET LYS ASN ALA THR ILE TYR ALA HIS SER PHE LEU ASP SEQRES 21 E 391 SER SER ILE PRO MET ILE THR THR GLY LYS GLY GLU ASN SEQRES 22 E 391 SER ILE VAL VAL SER ARG SER GLY ALA TYR SER GLU MET SEQRES 23 E 391 THR TYR ARG ASN GLY TYR GLU GLU ALA ILE ARG LEU GLN SEQRES 24 E 391 THR MET ALA GLN TYR ASP GLY TYR ALA LYS CYS SER THR SEQRES 25 E 391 ILE GLY ASN PHE ASN LEU THR PRO GLY VAL LYS ILE ILE SEQRES 26 E 391 PHE ASN ASP SER LYS ASN GLN PHE LYS THR GLU PHE TYR SEQRES 27 E 391 VAL ASP GLU VAL ILE HIS GLU LEU SER ASN ASN ASN SER SEQRES 28 E 391 VAL THR HIS LEU TYR MET PHE THR ASN ALA THR LYS LEU SEQRES 29 E 391 GLU THR ILE ASP PRO VAL LYS VAL LYS ASN GLU PHE LYS SEQRES 30 E 391 SER ASP THR THR THR GLU GLU SER SER SER SER ASN LYS SEQRES 31 E 391 GLN SEQRES 1 F 391 MET SER MET LEU GLN ARG PRO GLY TYR PRO ASN LEU SER SEQRES 2 F 391 VAL LYS LEU PHE ASP SER TYR ASP ALA TRP SER ASN ASN SEQRES 3 F 391 ARG PHE VAL GLU LEU ALA ALA THR ILE THR THR LEU THR SEQRES 4 F 391 MET ARG ASP SER LEU TYR GLY ARG ASN GLU GLY MET LEU SEQRES 5 F 391 GLN PHE TYR ASP SER LYS ASN ILE HIS THR LYS MET ASP SEQRES 6 F 391 GLY ASN GLU ILE ILE GLN ILE SER VAL ALA ASN ALA ASN SEQRES 7 F 391 ASP ILE ASN ASN VAL LYS THR ARG ILE TYR GLY CYS LYS SEQRES 8 F 391 HIS PHE SER VAL SER VAL ASP SER LYS GLY ASP ASN ILE SEQRES 9 F 391 ILE ALA ILE GLU LEU GLY THR ILE HIS SER ILE GLU ASN SEQRES 10 F 391 LEU LYS PHE GLY ARG PRO PHE PHE PRO ASP ALA GLY GLU SEQRES 11 F 391 SER ILE LYS GLU MET LEU GLY VAL ILE TYR GLN ASP ARG SEQRES 12 F 391 THR LEU LEU THR PRO ALA ILE ASN ALA ILE ASN ALA TYR SEQRES 13 F 391 VAL PRO ASP ILE PRO TRP THR SER THR PHE GLU ASN TYR SEQRES 14 F 391 LEU SER TYR VAL ARG GLU VAL ALA LEU ALA VAL GLY SER SEQRES 15 F 391 ASP LYS PHE VAL PHE VAL TRP GLN ASP ILE MET GLY VAL SEQRES 16 F 391 ASN MET MET ASP TYR ASP MET MET ILE ASN GLN GLU PRO SEQRES 17 F 391 TYR PRO MET ILE VAL GLY GLU PRO SER LEU ILE GLY GLN SEQRES 18 F 391 PHE ILE GLN GLU LEU LYS TYR PRO LEU ALA TYR ASP PHE SEQRES 19 F 391 VAL TRP LEU THR LYS SER ASN PRO HIS LYS ARG ASP PRO SEQRES 20 F 391 MET LYS ASN ALA THR ILE TYR ALA HIS SER PHE LEU ASP SEQRES 21 F 391 SER SER ILE PRO MET ILE THR THR GLY LYS GLY GLU ASN SEQRES 22 F 391 SER ILE VAL VAL SER ARG SER GLY ALA TYR SER GLU MET SEQRES 23 F 391 THR TYR ARG ASN GLY TYR GLU GLU ALA ILE ARG LEU GLN SEQRES 24 F 391 THR MET ALA GLN TYR ASP GLY TYR ALA LYS CYS SER THR SEQRES 25 F 391 ILE GLY ASN PHE ASN LEU THR PRO GLY VAL LYS ILE ILE SEQRES 26 F 391 PHE ASN ASP SER LYS ASN GLN PHE LYS THR GLU PHE TYR SEQRES 27 F 391 VAL ASP GLU VAL ILE HIS GLU LEU SER ASN ASN ASN SER SEQRES 28 F 391 VAL THR HIS LEU TYR MET PHE THR ASN ALA THR LYS LEU SEQRES 29 F 391 GLU THR ILE ASP PRO VAL LYS VAL LYS ASN GLU PHE LYS SEQRES 30 F 391 SER ASP THR THR THR GLU GLU SER SER SER SER ASN LYS SEQRES 31 F 391 GLN CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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