PDB Short entry for 4URD HEADER ISOMERASE 27-JUN-14 4URD TITLE CRYO-EM MAP OF TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIGGER FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RIBOSOME BINDING DOMAIN, RESIDUES 1-115; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, TRANSLATION, CO-TRANSLATIONAL PROTEIN FOLDING EXPDTA ELECTRON MICROSCOPY AUTHOR J.DEENG,K.Y.CHAN,E.VAN DER SLUIS,L.BISCHOFF,O.BERNINGHAUSEN,W.HAN, AUTHOR 2 J.GUMBART,K.SCHULTEN,B.BEATRIX,R.BECKMANN REVDAT 5 03-OCT-18 4URD 1 REMARK REVDAT 4 05-OCT-16 4URD 1 JRNL REVDAT 3 29-JUN-16 4URD 1 JRNL REVDAT 2 22-JUN-16 4URD 1 JRNL REVDAT 1 13-JAN-16 4URD 0 JRNL AUTH J.DEENG,K.Y.CHAN,E.O.VAN DER SLUIS,O.BERNINGHAUSEN,W.HAN, JRNL AUTH 2 J.GUMBART,K.SCHULTEN,B.BEATRIX,R.BECKMANN JRNL TITL DYNAMIC BEHAVIOR OF TRIGGER FACTOR ON THE RIBOSOME. JRNL REF J.MOL.BIOL. V. 428 3588 2016 JRNL REFN ISSN 0022-2836 JRNL PMID 27320387 JRNL DOI 10.1016/J.JMB.2016.06.007 REMARK 2 REMARK 2 RESOLUTION. 7.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER 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) : 7.700 REMARK 3 NUMBER OF PARTICLES : 100931 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD REMARK 3 -2695. (DEPOSITION ID: 12641). REMARK 4 REMARK 4 4URD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290061108. 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 : TNAC-STALLED-RNC WITH TRIGGER REMARK 245 FACTOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- CRYOGEN- REMARK 245 ETHANE, HUMIDITY- 100, REMARK 245 INSTRUMENT- FEI VITROBOT MARK REMARK 245 III, METHOD- BLOT FOR 10 REMARK 245 SECONDS BEFORE PLUNGING, USE 2 REMARK 245 LAYERS OF FILTER PAPER V, REMARK 245 SAMPLE BUFFER : 20 MM HEPES, 100 MM KOAC, 10 MM REMARK 245 MG(OAC)2, 2 MM DTT REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 21-NOV-10 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 39000 REMARK 245 CALIBRATED MAGNIFICATION : 38900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 ALA A 55 N - CA - CB ANGL. DEV. = 9.1 DEGREES REMARK 500 ASN A 74 N - CA - CB ANGL. DEV. = 14.6 DEGREES REMARK 500 ALA A 87 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 TYR A 105 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR A 105 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 VAL A 107 N - CA - CB ANGL. DEV. = 13.2 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 THR A 8 143.53 88.84 REMARK 500 GLN A 9 60.64 153.49 REMARK 500 LEU A 11 -21.09 81.65 REMARK 500 LYS A 29 -91.77 -71.45 REMARK 500 SER A 30 -95.86 -33.48 REMARK 500 GLU A 31 -75.69 -25.02 REMARK 500 LEU A 32 -84.53 -33.10 REMARK 500 VAL A 33 -72.25 -27.44 REMARK 500 ASN A 34 -76.79 -31.58 REMARK 500 ALA A 36 -75.87 -49.36 REMARK 500 LYS A 37 -87.59 -21.43 REMARK 500 VAL A 39 -35.38 160.36 REMARK 500 ARG A 40 -87.10 178.34 REMARK 500 ILE A 41 -173.29 47.06 REMARK 500 ASP A 42 -139.29 -119.24 REMARK 500 ARG A 45 -92.78 -88.19 REMARK 500 LYS A 46 -96.20 -84.63 REMARK 500 LYS A 48 6.99 -178.06 REMARK 500 VAL A 49 105.43 100.38 REMARK 500 ASN A 52 -135.63 45.16 REMARK 500 ALA A 55 -162.14 131.95 REMARK 500 MET A 71 -83.56 -45.02 REMARK 500 SER A 72 -60.65 -19.72 REMARK 500 LYS A 83 132.56 25.52 REMARK 500 ALA A 87 117.76 174.02 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 ARG A 73 0.09 SIDE CHAIN REMARK 500 TYR A 97 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-2695 RELATED DB: EMDB DBREF 4URD A 1 115 UNP I4UK46 I4UK46_ECOLX 1 115 SEQRES 1 A 115 MET GLN VAL SER VAL GLU THR THR GLN GLY LEU GLY ARG SEQRES 2 A 115 ARG VAL THR ILE THR ILE ALA ALA ASP SER ILE GLU THR SEQRES 3 A 115 ALA VAL LYS SER GLU LEU VAL ASN VAL ALA LYS LYS VAL SEQRES 4 A 115 ARG ILE ASP GLY PHE ARG LYS GLY LYS VAL PRO MET ASN SEQRES 5 A 115 ILE VAL ALA GLN ARG TYR GLY ALA SER VAL ARG GLN ASP SEQRES 6 A 115 VAL LEU GLY ASP LEU MET SER ARG ASN PHE ILE ASP ALA SEQRES 7 A 115 ILE ILE LYS GLU LYS ILE ASN PRO ALA GLY ALA PRO THR SEQRES 8 A 115 TYR VAL PRO GLY GLU TYR LYS LEU GLY GLU ASP PHE THR SEQRES 9 A 115 TYR SER VAL GLU PHE GLU VAL TYR PRO GLU VAL HELIX 1 1 ALA A 21 LYS A 29 1 9 HELIX 2 2 LYS A 29 LYS A 38 1 10 HELIX 3 3 GLN A 56 GLU A 82 1 27 SHEET 1 AA 2 GLN A 2 THR A 7 0 SHEET 2 AA 2 ARG A 13 THR A 18 -1 O ARG A 14 N GLU A 6 SHEET 1 AB 2 THR A 91 PRO A 94 0 SHEET 2 AB 2 TYR A 105 GLU A 108 -1 O SER A 106 N VAL A 93 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