HEADER CELL CYCLE/PROTEIN FIBRIL 04-FEB-08 2ZHC TITLE PARM FILAMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMID SEGREGATION PROTEIN PARM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN STBA, PARA LOCUS 36 KDA PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PARM, STBA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMD137 KEYWDS PARM, PLASMID, PLASMID PARTITION, CELL CYCLE-PROTEIN FIBRIL COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR D.POPP,A.NARITA,T.ODA,T.FUJISAWA,H.MATSUO,Y.NITANAI,M.IWASA,K.MAEDA, AUTHOR 2 H.ONISHI,Y.MAEDA REVDAT 4 13-MAR-24 2ZHC 1 REMARK LINK REVDAT 3 18-DEC-19 2ZHC 1 REMARK REVDAT 2 24-FEB-09 2ZHC 1 VERSN REVDAT 1 26-FEB-08 2ZHC 0 JRNL AUTH D.POPP,A.NARITA,T.ODA,T.FUJISAWA,H.MATSUO,Y.NITANAI,M.IWASA, JRNL AUTH 2 K.MAEDA,H.ONISHI JRNL TITL MOLECULAR STRUCTURE OF THE PARM POLYMER AND THE MECHANISM JRNL TITL 2 LEADING TO ITS NUCLEOTIDE-DRIVEN DYNAMIC INSTABILITY JRNL REF EMBO J. V. 27 570 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18188150 JRNL DOI 10.1038/SJ.EMBOJ.7601978 REMARK 2 REMARK 2 RESOLUTION. 23.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EOS REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1MWM 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) : 4.011 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 23.00 REMARK 3 NUMBER OF PARTICLES : 2085 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THIS DATA WAS ACHIEVED BY NEGATIVE STAINING REMARK 3 EXPERIMENTS REMARK 4 REMARK 4 2ZHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000027972. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NEGATIVE STAIN REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : PARM FILAMENT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.13 REMARK 245 SAMPLE SUPPORT DETAILS : CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : 10MM HEPES, 25MM KCL, 1MM REMARK 245 MGCL2, 1MM DTT, 5MM GMPPNP REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : STAINED WITH 1.0 % URANYL REMARK 245 ACETATE REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JAN-07 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 300.00 REMARK 245 MICROSCOPE MODEL : JEOL 2010HC REMARK 245 DETECTOR TYPE : GENERIC FILM REMARK 245 MINIMUM DEFOCUS (NM) : 3700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 10300.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1200.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 40000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : LAB6 REMARK 245 ACCELERATION VOLTAGE (KV) : 100 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: MONOMERIC 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 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 OD1 ASP A 76 HZ2 LYS A 128 1.52 REMARK 500 OE1 GLU A 120 HZ2 LYS A 123 1.53 REMARK 500 H3 MET A 1 OD2 ASP A 97 1.54 REMARK 500 HZ3 LYS A 13 O2B ADP A 500 1.57 REMARK 500 OD2 ASP A 7 HZ2 LYS A 122 1.57 REMARK 500 HZ1 LYS A 291 OD2 ASP A 298 1.58 REMARK 500 OE1 GLU A 162 HZ3 LYS A 184 1.59 REMARK 500 OE2 GLU A 18 HZ2 LYS A 24 1.59 REMARK 500 HZ2 LYS A 230 OE1 GLU A 284 1.59 REMARK 500 OD2 ASP A 208 HH12 ARG A 214 1.60 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 170 OD1 - CG - OD2 ANGL. DEV. = -11.5 DEGREES REMARK 500 ASP A 170 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 170 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 229 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 238 NE - CZ - NH2 ANGL. DEV. = 3.6 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 ASP A 7 50.72 -90.99 REMARK 500 GLU A 18 -161.88 -117.44 REMARK 500 SER A 31 60.35 -157.71 REMARK 500 ASP A 42 -73.14 -60.14 REMARK 500 LYS A 43 90.96 -59.51 REMARK 500 LEU A 50 -83.02 -98.13 REMARK 500 THR A 67 -87.22 -123.58 REMARK 500 VAL A 93 99.30 -46.77 REMARK 500 SER A 94 -100.73 -161.89 REMARK 500 ASP A 109 -159.24 -78.23 REMARK 500 PHE A 126 32.88 -74.45 REMARK 500 LYS A 141 -76.71 -80.57 REMARK 500 GLU A 148 -71.51 -63.82 REMARK 500 THR A 174 -62.18 -104.42 REMARK 500 LYS A 184 13.84 57.71 REMARK 500 SER A 189 -113.56 -99.03 REMARK 500 SER A 195 32.08 -155.90 REMARK 500 LEU A 210 -117.49 -74.79 REMARK 500 SER A 211 29.56 -152.26 REMARK 500 SER A 218 43.33 -87.40 REMARK 500 HIS A 228 29.96 -79.55 REMARK 500 ASP A 241 130.85 -173.47 REMARK 500 PHE A 270 81.66 -69.33 REMARK 500 THR A 274 -46.21 -136.66 REMARK 500 ALA A 289 -70.16 -80.99 REMARK 500 THR A 304 -152.05 -91.24 REMARK 500 SER A 307 -67.32 79.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 95 VAL A 96 136.88 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 TYR A 74 0.12 SIDE CHAIN REMARK 500 ARG A 121 0.10 SIDE CHAIN REMARK 500 ARG A 127 0.25 SIDE CHAIN REMARK 500 TYR A 220 0.11 SIDE CHAIN REMARK 500 ARG A 238 0.09 SIDE CHAIN REMARK 500 ARG A 257 0.10 SIDE CHAIN REMARK 500 ARG A 300 0.11 SIDE CHAIN REMARK 500 TYR A 316 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 170 OD1 REMARK 620 2 ASP A 170 OD2 67.8 REMARK 620 3 ADP A 500 O2B 151.5 105.6 REMARK 620 4 ADP A 500 O3B 104.6 163.7 73.9 REMARK 620 5 ADP A 500 O1A 115.7 103.2 92.8 93.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MWM RELATED DB: PDB REMARK 900 COORDINATES OF FITTING STRUCTURE REMARK 900 RELATED ID: EMD-1470 RELATED DB: EMDB DBREF 2ZHC A 1 320 UNP P11904 PARM_ECOLX 1 320 SEQRES 1 A 320 MET LEU VAL PHE ILE ASP ASP GLY SER THR ASN ILE LYS SEQRES 2 A 320 LEU GLN TRP GLN GLU SER ASP GLY THR ILE LYS GLN HIS SEQRES 3 A 320 ILE SER PRO ASN SER PHE LYS ARG GLU TRP ALA VAL SER SEQRES 4 A 320 PHE GLY ASP LYS LYS VAL PHE ASN TYR THR LEU ASN GLY SEQRES 5 A 320 GLU GLN TYR SER PHE ASP PRO ILE SER PRO ASP ALA VAL SEQRES 6 A 320 VAL THR THR ASN ILE ALA TRP GLN TYR SER ASP VAL ASN SEQRES 7 A 320 VAL VAL ALA VAL HIS HIS ALA LEU LEU THR SER GLY LEU SEQRES 8 A 320 PRO VAL SER GLU VAL ASP ILE VAL CYS THR LEU PRO LEU SEQRES 9 A 320 THR GLU TYR TYR ASP ARG ASN ASN GLN PRO ASN THR GLU SEQRES 10 A 320 ASN ILE GLU ARG LYS LYS ALA ASN PHE ARG LYS LYS ILE SEQRES 11 A 320 THR LEU ASN GLY GLY ASP THR PHE THR ILE LYS ASP VAL SEQRES 12 A 320 LYS VAL MET PRO GLU SER ILE PRO ALA GLY TYR GLU VAL SEQRES 13 A 320 LEU GLN GLU LEU ASP GLU LEU ASP SER LEU LEU ILE ILE SEQRES 14 A 320 ASP LEU GLY GLY THR THR LEU ASP ILE SER GLN VAL MET SEQRES 15 A 320 GLY LYS LEU SER GLY ILE SER LYS ILE TYR GLY ASP SER SEQRES 16 A 320 SER LEU GLY VAL SER LEU VAL THR SER ALA VAL LYS ASP SEQRES 17 A 320 ALA LEU SER LEU ALA ARG THR LYS GLY SER SER TYR LEU SEQRES 18 A 320 ALA ASP ASP ILE ILE ILE HIS ARG LYS ASP ASN ASN TYR SEQRES 19 A 320 LEU LYS GLN ARG ILE ASN ASP GLU ASN LYS ILE SER ILE SEQRES 20 A 320 VAL THR GLU ALA MET ASN GLU ALA LEU ARG LYS LEU GLU SEQRES 21 A 320 GLN ARG VAL LEU ASN THR LEU ASN GLU PHE SER GLY TYR SEQRES 22 A 320 THR HIS VAL MET VAL ILE GLY GLY GLY ALA GLU LEU ILE SEQRES 23 A 320 CYS ASP ALA VAL LYS LYS HIS THR GLN ILE ARG ASP GLU SEQRES 24 A 320 ARG PHE PHE LYS THR ASN ASN SER GLN TYR ASP LEU VAL SEQRES 25 A 320 ASN GLY MET TYR LEU ILE GLY ASN HET MG A 501 1 HET ADP A 500 39 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 ADP C10 H15 N5 O10 P2 HELIX 1 1 THR A 68 GLN A 73 1 6 HELIX 2 2 SER A 75 GLY A 90 1 16 HELIX 3 3 PRO A 103 TYR A 108 1 6 HELIX 4 4 ASN A 115 PHE A 126 1 12 HELIX 5 5 SER A 149 ALA A 152 5 4 HELIX 6 6 GLY A 153 GLN A 158 1 6 HELIX 7 7 LYS A 184 SER A 186 5 3 HELIX 8 8 GLY A 198 LEU A 210 1 13 HELIX 9 9 SER A 219 HIS A 228 1 10 HELIX 10 10 ARG A 229 ASP A 231 5 3 HELIX 11 11 ASN A 232 ILE A 239 1 8 HELIX 12 12 ASP A 241 PHE A 270 1 30 HELIX 13 13 GLY A 282 GLN A 295 1 14 HELIX 14 14 ARG A 297 GLU A 299 5 3 HELIX 15 15 GLN A 308 LEU A 317 1 10 SHEET 1 A 5 ILE A 23 PRO A 29 0 SHEET 2 A 5 ASN A 11 GLN A 17 -1 N ILE A 12 O SER A 28 SHEET 3 A 5 LEU A 2 ASP A 6 -1 N PHE A 4 O GLN A 15 SHEET 4 A 5 GLU A 95 LEU A 102 1 O ASP A 97 N VAL A 3 SHEET 5 A 5 THR A 139 PRO A 147 1 O LYS A 144 N ILE A 98 SHEET 1 B 4 PHE A 32 LYS A 33 0 SHEET 2 B 4 GLN A 54 PHE A 57 -1 O SER A 56 N LYS A 33 SHEET 3 B 4 ASN A 47 THR A 49 -1 N TYR A 48 O TYR A 55 SHEET 4 B 4 THR A 131 LEU A 132 -1 O THR A 131 N THR A 49 SHEET 1 C 5 ILE A 188 TYR A 192 0 SHEET 2 C 5 ILE A 178 MET A 182 -1 N GLN A 180 O SER A 189 SHEET 3 C 5 SER A 165 ASP A 170 -1 N LEU A 166 O VAL A 181 SHEET 4 C 5 HIS A 275 ILE A 279 1 O MET A 277 N LEU A 167 SHEET 5 C 5 PHE A 301 PHE A 302 1 O PHE A 302 N VAL A 278 LINK OD1 ASP A 170 MG MG A 501 1555 1555 1.86 LINK OD2 ASP A 170 MG MG A 501 1555 1555 1.87 LINK O2B ADP A 500 MG MG A 501 1555 1555 1.85 LINK O3B ADP A 500 MG MG A 501 1555 1555 1.81 LINK O1A ADP A 500 MG MG A 501 1555 1555 1.86 SITE 1 AC1 2 THR A 10 GLY A 280 SITE 1 AC2 12 GLY A 8 SER A 9 THR A 10 ASN A 11 SITE 2 AC2 12 LEU A 171 GLY A 173 ASP A 223 ILE A 226 SITE 3 AC2 12 ILE A 227 ARG A 229 GLY A 280 GLU A 284 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