HEADER VIRAL PROTEIN 20-NOV-13 3J5V TITLE PHUZ201 FILAMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHUZ201 SUBUNIT; COMPND 3 CHAIN: a; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE 201PHI2-1; SOURCE 3 ORGANISM_TAXID: 198110; SOURCE 4 GENE: 201PHI2-1P059; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS PHUZ, TUBULIN, FTSZ, FILAMENT, BACTERIOPHAGE, CYTOSKELETON, KEYWDS 2 BACTERIOPHAGE CENTERING FUNCTION, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR E.A.ZEHR REVDAT 5 21-FEB-24 3J5V 1 REMARK SEQADV REVDAT 4 18-JUL-18 3J5V 1 REMARK REVDAT 3 23-APR-14 3J5V 1 REMARK REVDAT 2 09-APR-14 3J5V 1 REMARK REVDAT 1 26-MAR-14 3J5V 0 JRNL AUTH E.A.ZEHR,J.K.KRAEMER,M.L.ERB,J.K.C.COKER,E.A.MONTABANA, JRNL AUTH 2 J.POGLIANO,D.A.AGARD JRNL TITL THE STRUCTURE AND ASSEMBLY MECHANISM OF A NOVEL JRNL TITL 2 THREE-STRANDED TUBULIN FILAMENT THAT CENTERS PHAGE DNA JRNL REF STRUCTURE V. 22 1 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24631461 JRNL DOI 10.1016/J.STR.2014.02.006 REMARK 2 REMARK 2 RESOLUTION. 7.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, UCSF CHIMERA, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3R4V REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--FLEXIBLE FITTING DETAILS--FLEXIBLE REMARK 3 FITTING APPLIED TO C-TERMINUS (RESIDUES 273-315) REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.204 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 7.100 REMARK 3 NUMBER OF PARTICLES : 23243 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: A MODIFIED VERSION OF SPIDER PROGRAM WAS USED FOR REMARK 3 THE RECONSTRUCTION. HELICAL SYMMETRY SEARCH WAS PERFORMED WITH REMARK 3 HSEARCH_LORENTZ. REMARK 4 REMARK 4 3J5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000160289. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : PHUZ FILAMENT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.70 REMARK 245 SAMPLE SUPPORT DETAILS : C-FLAT HOLEY CARBON GRID, 200 REMARK 245 MESH COPPER GRID REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTED 2 SECONDS BEFORE REMARK 245 PLUNGING IN LIQUID ETHANE (FEI REMARK 245 VITROBOT MARK III) REMARK 245 SAMPLE BUFFER : 250 MM KCL, 50 MM HEPES PH 7.4, REMARK 245 1 MM MGCL2, 10% GLYCEROL, 1MM REMARK 245 DTT REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 21-NOV-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : TVIPS TEMCAM-F816 (8K X 8K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.20 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 : 62000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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) = -116.44 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 14.42 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 -0.271608 -0.962408 0.000000 0.00000 REMARK 350 BIOMT2 1 0.962408 -0.271608 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -57.68000 REMARK 350 BIOMT1 2 0.982678 0.185324 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.185324 0.982678 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -43.26000 REMARK 350 BIOMT1 3 -0.603486 0.797373 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.797373 -0.603486 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -28.84000 REMARK 350 BIOMT1 4 -0.445260 -0.895401 0.000000 0.00000 REMARK 350 BIOMT2 4 0.895401 -0.445260 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -14.42000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.445260 0.895401 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.895401 -0.445260 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 14.42000 REMARK 350 BIOMT1 7 -0.603486 -0.797373 0.000000 0.00000 REMARK 350 BIOMT2 7 0.797373 -0.603486 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 28.84000 REMARK 350 BIOMT1 8 0.982678 -0.185324 0.000000 0.00000 REMARK 350 BIOMT2 8 0.185324 0.982678 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 43.26000 REMARK 350 BIOMT1 9 -0.271608 0.962408 0.000000 0.00000 REMARK 350 BIOMT2 9 -0.962408 -0.271608 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 57.68000 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 -4 REMARK 465 SER a -3 REMARK 465 HIS a -2 REMARK 465 MET a -1 REMARK 465 ALA a 0 REMARK 465 SER a 1 REMARK 465 GLY a 55 REMARK 465 ALA a 56 REMARK 465 GLY a 57 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 O THR a 289 OG SER a 293 2.03 REMARK 500 O SER a 293 N PHE a 295 2.09 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 ASP a 306 O - C - N ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP a 306 O - C - N ANGL. DEV. = 10.8 DEGREES REMARK 500 ASN a 307 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 ASN a 307 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 VAL a 308 C - N - CA ANGL. DEV. = 16.6 DEGREES REMARK 500 VAL a 308 C - N - CA ANGL. DEV. = 17.4 DEGREES REMARK 500 GLU a 310 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 GLU a 310 N - CA - C ANGL. DEV. = 17.9 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 ARG a 185 -9.53 76.16 REMARK 500 ARG a 196 52.74 -97.48 REMARK 500 HIS a 201 76.36 -108.38 REMARK 500 HIS a 201 76.29 -108.38 REMARK 500 SER a 271 -9.31 -145.60 REMARK 500 VAL a 272 34.54 -85.13 REMARK 500 LYS a 294 66.64 -45.20 REMARK 500 THR a 296 88.19 -157.76 REMARK 500 ALA a 304 0.96 -62.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP a 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG a 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5783 RELATED DB: EMDB REMARK 900 CRYO-EM MAP OF PHUZ201 FILAMENT REMARK 900 RELATED ID: 3R4V RELATED DB: PDB REMARK 900 STRUCTURE OF THE PHAGE TUBULIN PHUZ-GDP DBREF 3J5V a 2 315 UNP B3FK34 B3FK34_9CAUD 2 315 SEQADV 3J5V GLY a -4 UNP B3FK34 EXPRESSION TAG SEQADV 3J5V SER a -3 UNP B3FK34 EXPRESSION TAG SEQADV 3J5V HIS a -2 UNP B3FK34 EXPRESSION TAG SEQADV 3J5V MET a -1 UNP B3FK34 EXPRESSION TAG SEQADV 3J5V ALA a 0 UNP B3FK34 EXPRESSION TAG SEQADV 3J5V SER a 1 UNP B3FK34 EXPRESSION TAG SEQRES 1 a 320 GLY SER HIS MET ALA SER PRO VAL LYS VAL CYS LEU ILE SEQRES 2 a 320 PHE ALA GLY GLY THR GLY MET ASN VAL ALA THR LYS LEU SEQRES 3 a 320 VAL ASP LEU GLY GLU ALA VAL HIS CYS PHE ASP THR CYS SEQRES 4 a 320 ASP LYS ASN VAL VAL ASP VAL HIS ARG SER VAL ASN VAL SEQRES 5 a 320 THR LEU THR LYS GLY THR ARG GLY ALA GLY GLY ASN ARG SEQRES 6 a 320 LYS VAL ILE LEU PRO LEU VAL ARG PRO GLN ILE PRO ALA SEQRES 7 a 320 LEU MET ASP THR ILE PRO GLU ALA ASP PHE TYR ILE VAL SEQRES 8 a 320 CYS TYR SER LEU GLY GLY GLY SER GLY SER VAL LEU GLY SEQRES 9 a 320 PRO LEU ILE THR GLY GLN LEU ALA ASP ARG LYS ALA SER SEQRES 10 a 320 PHE VAL SER PHE VAL VAL GLY ALA MET GLU SER THR ASP SEQRES 11 a 320 ASN LEU GLY ASN ASP ILE ASP THR MET LYS THR LEU GLU SEQRES 12 a 320 ALA ILE ALA VAL ASN LYS HIS LEU PRO ILE VAL VAL ASN SEQRES 13 a 320 TYR VAL PRO ASN THR GLN GLY ARG SER TYR GLU SER ILE SEQRES 14 a 320 ASN ASP GLU ILE ALA GLU LYS ILE ARG LYS VAL VAL LEU SEQRES 15 a 320 LEU VAL ASN GLN ASN HIS GLY ARG LEU ASP VAL HIS ASP SEQRES 16 a 320 VAL ALA ASN TRP VAL ARG PHE THR ASP LYS HIS ASN TYR SEQRES 17 a 320 LEU ILE PRO GLN VAL CYS GLU LEU HIS ILE GLU THR THR SEQRES 18 a 320 ARG LYS ASP ALA GLU ASN VAL PRO GLU ALA ILE SER GLN SEQRES 19 a 320 LEU SER LEU TYR LEU ASP PRO SER LYS GLU VAL ALA PHE SEQRES 20 a 320 GLY THR PRO ILE TYR ARG LYS VAL GLY ILE MET LYS VAL SEQRES 21 a 320 ASP ASP LEU ASP VAL THR ASP ASP GLN ILE HIS PHE VAL SEQRES 22 a 320 ILE ASN SER VAL GLY VAL VAL GLU ILE MET LYS THR ILE SEQRES 23 a 320 THR ASP SER LYS LEU GLU MET THR ARG GLN GLN SER LYS SEQRES 24 a 320 PHE THR GLN ARG ASN PRO ILE ILE ASP ALA ASP ASP ASN SEQRES 25 a 320 VAL ASP GLU ASP GLY MET VAL VAL HET GDP a 401 28 HET MG a 402 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ HELIX 1 1 GLY a 11 THR a 19 1 9 HELIX 2 2 LYS a 20 GLU a 26 5 7 HELIX 3 3 VAL a 39 VAL a 45 5 7 HELIX 4 4 ASN a 59 ARG a 68 1 10 HELIX 5 5 GLN a 70 THR a 77 1 8 HELIX 6 6 SER a 94 ARG a 109 1 16 HELIX 7 7 SER a 123 HIS a 145 1 23 HELIX 8 8 SER a 160 VAL a 179 1 20 HELIX 9 9 ASP a 187 ARG a 196 1 10 HELIX 10 10 PHE a 197 LYS a 200 5 4 HELIX 11 11 THR a 216 ASN a 222 1 7 HELIX 12 12 ASP a 235 GLU a 239 5 5 HELIX 13 13 GLY a 273 LYS a 294 1 22 SHEET 1 A10 ASN a 46 LEU a 49 0 SHEET 2 A10 VAL a 28 ASP a 32 1 N CYS a 30 O THR a 48 SHEET 3 A10 CYS a 6 ALA a 10 1 N LEU a 7 O HIS a 29 SHEET 4 A10 TYR a 84 SER a 89 1 O ILE a 85 N ILE a 8 SHEET 5 A10 PHE a 113 GLY a 119 1 O PHE a 116 N VAL a 86 SHEET 6 A10 ILE a 148 PRO a 154 1 O ASN a 151 N SER a 115 SHEET 7 A10 VAL a 208 GLU a 214 1 O CYS a 209 N VAL a 150 SHEET 8 A10 GLN a 264 ASN a 270 -1 O HIS a 266 N GLU a 214 SHEET 9 A10 SER a 228 TYR a 233 -1 N LEU a 230 O PHE a 267 SHEET 10 A10 TYR a 247 ILE a 252 1 O GLY a 251 N SER a 231 LINK O2B GDP a 401 MG MG a 402 1555 1555 2.21 SITE 1 AC1 18 GLY a 11 GLY a 12 THR a 13 ASN a 16 SITE 2 AC1 18 SER a 89 GLY a 92 GLY a 93 SER a 94 SITE 3 AC1 18 GLY a 95 VAL a 118 ALA a 120 GLU a 122 SITE 4 AC1 18 ASN a 126 ASN a 155 TYR a 161 ILE a 164 SITE 5 AC1 18 ASN a 165 MG a 402 SITE 1 AC2 1 GDP a 401 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