HEADER TRANSLATION 11-JUL-19 6S8Z TITLE ELONGATION FACTOR P FROM CORYNEBACTERIUM GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR P; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EF-P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 3 ORGANISM_TAXID: 1718; SOURCE 4 GENE: EFP, CS176_1554; SOURCE 5 EXPRESSION_SYSTEM: CORYNEBACTERIUM GLUTAMICUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1718 KEYWDS ELONGATION FACTOR P, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHNEIDER,C.M.SCHEIDLER REVDAT 3 24-JAN-24 6S8Z 1 REMARK REVDAT 2 08-APR-20 6S8Z 1 JRNL REVDAT 1 26-FEB-20 6S8Z 0 JRNL AUTH B.PINHEIRO,C.M.SCHEIDLER,P.KIELKOWSKI,M.SCHMID,I.FORNE,S.YE, JRNL AUTH 2 N.REILING,E.TAKANO,A.IMHOF,S.A.SIEBER,S.SCHNEIDER,K.JUNG JRNL TITL STRUCTURE AND FUNCTION OF AN ELONGATION FACTOR P SUBFAMILY JRNL TITL 2 IN ACTINOBACTERIA. JRNL REF CELL REP V. 30 4332 2020 JRNL REFN ESSN 2211-1247 JRNL PMID 32234471 JRNL DOI 10.1016/J.CELREP.2020.03.009 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 10928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 1475 REMARK 3 ANGLE : 1.721 1989 REMARK 3 CHIRALITY : 0.097 225 REMARK 3 PLANARITY : 0.005 263 REMARK 3 DIHEDRAL : 13.253 875 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6S8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 2.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3OYY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE 0.1 M HEPES PH REMARK 280 7.5 22 %(W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.08150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 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 A 1 REMARK 465 THR A 146 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 LEU A 73 -61.12 -94.01 REMARK 500 THR A 78 -54.52 -125.43 REMARK 500 ARG A 103 -37.60 -29.23 REMARK 500 ASP A 178 16.86 -151.09 REMARK 500 LEU A 182 -62.58 -102.67 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 ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 DBREF1 6S8Z A 1 187 UNP A0A1B4WLR4_CORGT DBREF2 6S8Z A A0A1B4WLR4 1 187 SEQRES 1 A 187 MET ALA THR THR ALA ASP PHE LYS ASN GLY LEU VAL LEU SEQRES 2 A 187 LYS ASN GLU GLY LYS LEU GLN GLN ILE ILE GLU PHE GLN SEQRES 3 A 187 HIS VAL LYS PRO GLY LYS GLY PRO ALA PHE VAL ARG THR SEQRES 4 A 187 LYS LEU LYS ASP VAL VAL THR GLY LYS THR ILE ASP LYS SEQRES 5 A 187 THR TRP ASN ALA GLY VAL LYS VAL GLU THR ALA THR VAL SEQRES 6 A 187 ASP ARG ARG ASP VAL THR TYR LEU TYR ASN ASP GLY THR SEQRES 7 A 187 SER PHE ILE VAL MET ASP ASP LYS THR PHE GLU GLN TYR SEQRES 8 A 187 GLU LEU SER PRO ASP ALA PHE GLY ASP ALA GLY ARG PHE SEQRES 9 A 187 LEU LEU GLU ASN MET ARG VAL GLN VAL SER PHE HIS GLU SEQRES 10 A 187 GLY GLU ALA LEU PHE GLY GLU LEU PRO VAL SER VAL ASP SEQRES 11 A 187 LEU ARG VAL GLU HIS THR ASP PRO GLY LEU GLN GLY ASP SEQRES 12 A 187 ARG SER THR GLY GLY THR LYS PRO ALA THR LEU GLU THR SEQRES 13 A 187 GLY ALA GLU ILE GLN VAL PRO LEU PHE ILE GLU THR GLY SEQRES 14 A 187 ASN VAL LEU LYS VAL ASP THR ARG ASP GLY SER TYR LEU SEQRES 15 A 187 SER ARG VAL ASN ASN HET ACT A 201 4 HET ACT A 202 4 HET ACT A 203 4 HET EDO A 204 4 HET NA A 205 1 HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ACT 3(C2 H3 O2 1-) FORMUL 5 EDO C2 H6 O2 FORMUL 6 NA NA 1+ FORMUL 7 HOH *56(H2 O) HELIX 1 AA1 THR A 3 PHE A 7 5 5 HELIX 2 AA2 PHE A 98 LEU A 105 5 8 SHEET 1 AA1 5 THR A 49 ASN A 55 0 SHEET 2 AA1 5 PHE A 36 ASP A 43 -1 N LEU A 41 O ILE A 50 SHEET 3 AA1 5 LYS A 18 VAL A 28 -1 N VAL A 28 O PHE A 36 SHEET 4 AA1 5 VAL A 12 ASN A 15 -1 N LEU A 13 O GLN A 20 SHEET 5 AA1 5 GLU A 61 THR A 62 -1 O GLU A 61 N LYS A 14 SHEET 1 AA2 5 GLN A 90 LEU A 93 0 SHEET 2 AA2 5 PHE A 80 ASP A 84 -1 N VAL A 82 O TYR A 91 SHEET 3 AA2 5 ASP A 66 ASN A 75 -1 N TYR A 74 O ILE A 81 SHEET 4 AA2 5 ARG A 110 HIS A 116 -1 O VAL A 111 N VAL A 70 SHEET 5 AA2 5 GLU A 119 GLU A 124 -1 O LEU A 121 N SER A 114 SHEET 1 AA3 5 GLU A 159 PRO A 163 0 SHEET 2 AA3 5 THR A 149 LEU A 154 -1 N ALA A 152 O ILE A 160 SHEET 3 AA3 5 SER A 128 THR A 136 -1 N HIS A 135 O THR A 153 SHEET 4 AA3 5 VAL A 171 ASP A 175 -1 O VAL A 174 N VAL A 129 SHEET 5 AA3 5 SER A 180 VAL A 185 -1 O SER A 183 N LYS A 173 SITE 1 AC1 2 LEU A 182 SER A 183 SITE 1 AC2 4 ASN A 75 GLY A 77 THR A 78 PRO A 95 SITE 1 AC3 3 LYS A 18 LEU A 19 ASP A 43 SITE 1 AC4 5 GLN A 141 PHE A 165 GLU A 167 ARG A 184 SITE 2 AC4 5 HOH A 337 SITE 1 AC5 1 PHE A 80 CRYST1 51.201 38.163 55.356 90.00 93.09 90.00 P 1 21 1 2 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 0.019531 0.000000 0.001054 0.00000 SCALE2 0.000000 0.026203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018091 0.00000