HEADER TRANSLATION 27-APR-19 6RJI TITLE X-RAY STRUCTURE OF THE ELONGATION FACTOR P OF S. AUREUS 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: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325); SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 GENE: EFP, SAOUHSC_01625; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS ELONGATION FACTOR P, EFP, EF-P, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR B.F.FATKHULLIN,A.A.GOLUBEV,A.G.GABDULKHAKOV,I.S.KHUSAINOV, AUTHOR 2 S.Z.VALIDOV,K.S.USACHEV,G.YUSUPOVA,M.M.YUSUPOV REVDAT 3 24-JAN-24 6RJI 1 REMARK REVDAT 2 03-JUN-20 6RJI 1 JRNL REVDAT 1 01-APR-20 6RJI 0 JRNL AUTH A.GOLUBEV,B.FATKHULLIN,A.GABDULKHAKOV,A.BIKMULLIN, JRNL AUTH 2 L.NURULLINA,N.GARAEVA,D.ISLAMOV,E.KLOCHKOVA,V.KLOCHKOV, JRNL AUTH 3 A.AGANOV,I.KHUSAINOV,S.VALIDOV,G.YUSUPOVA,M.YUSUPOV, JRNL AUTH 4 K.USACHEV JRNL TITL NMR AND CRYSTALLOGRAPHIC STRUCTURAL STUDIES OF THE JRNL TITL 2 ELONGATION FACTOR P FROM STAPHYLOCOCCUS AUREUS. JRNL REF EUR.BIOPHYS.J. V. 49 223 2020 JRNL REFN ISSN 0175-7571 JRNL PMID 32152681 JRNL DOI 10.1007/S00249-020-01428-X REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.1124 - 3.1882 1.00 2926 154 0.1841 0.2003 REMARK 3 2 3.1882 - 2.5306 1.00 2748 145 0.2075 0.2452 REMARK 3 3 2.5306 - 2.2108 1.00 2751 145 0.1858 0.2144 REMARK 3 4 2.2108 - 2.0087 1.00 2717 143 0.1524 0.2299 REMARK 3 5 2.0087 - 1.8647 1.00 2722 143 0.1486 0.2131 REMARK 3 6 1.8647 - 1.7547 1.00 2673 141 0.1519 0.2304 REMARK 3 7 1.7547 - 1.6669 1.00 2668 140 0.1477 0.2360 REMARK 3 8 1.6669 - 1.5943 1.00 2681 141 0.1542 0.2499 REMARK 3 9 1.5943 - 1.5329 1.00 2706 143 0.1809 0.2717 REMARK 3 10 1.5329 - 1.4800 1.00 2671 141 0.2187 0.2899 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1964 REMARK 3 ANGLE : 0.884 2680 REMARK 3 CHIRALITY : 0.083 298 REMARK 3 PLANARITY : 0.005 361 REMARK 3 DIHEDRAL : 16.347 740 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 6RJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292102036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04586 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.75150 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.970 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: 1YBY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M IMIDAZOLE MALATE 24% PEG600 PH REMARK 280 5.5, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.13300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.17150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.17150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.13300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.73000 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 LYS A 141 REMARK 465 GLY A 142 REMARK 465 ASP A 143 REMARK 465 THR A 144 REMARK 465 ALA A 145 REMARK 465 THR A 146 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE 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 LYS A 59 75.87 69.77 REMARK 500 LYS A 99 -89.42 35.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 6RJI A 1 185 UNP Q2FY41 EFP_STAA8 1 185 SEQADV 6RJI HIS A 186 UNP Q2FY41 EXPRESSION TAG SEQADV 6RJI HIS A 187 UNP Q2FY41 EXPRESSION TAG SEQADV 6RJI HIS A 188 UNP Q2FY41 EXPRESSION TAG SEQADV 6RJI HIS A 189 UNP Q2FY41 EXPRESSION TAG SEQADV 6RJI HIS A 190 UNP Q2FY41 EXPRESSION TAG SEQADV 6RJI HIS A 191 UNP Q2FY41 EXPRESSION TAG SEQRES 1 A 191 MET ILE SER VAL ASN ASP PHE LYS THR GLY LEU THR ILE SEQRES 2 A 191 SER VAL ASP ASN ALA ILE TRP LYS VAL ILE ASP PHE GLN SEQRES 3 A 191 HIS VAL LYS PRO GLY LYS GLY SER ALA PHE VAL ARG SER SEQRES 4 A 191 LYS LEU ARG ASN LEU ARG THR GLY ALA ILE GLN GLU LYS SEQRES 5 A 191 THR PHE ARG ALA GLY GLU LYS VAL GLU PRO ALA MET ILE SEQRES 6 A 191 GLU ASN ARG ARG MET GLN TYR LEU TYR ALA ASP GLY ASP SEQRES 7 A 191 ASN HIS VAL PHE MET ASP ASN GLU SER PHE GLU GLN THR SEQRES 8 A 191 GLU LEU SER SER ASP TYR LEU LYS GLU GLU LEU ASN TYR SEQRES 9 A 191 LEU LYS GLU GLY MET GLU VAL GLN ILE GLN THR TYR GLU SEQRES 10 A 191 GLY GLU THR ILE GLY VAL GLU LEU PRO LYS THR VAL GLU SEQRES 11 A 191 LEU THR VAL THR GLU THR GLU PRO GLY ILE LYS GLY ASP SEQRES 12 A 191 THR ALA THR GLY ALA THR LYS SER ALA THR VAL GLU THR SEQRES 13 A 191 GLY TYR THR LEU ASN VAL PRO LEU PHE VAL ASN GLU GLY SEQRES 14 A 191 ASP VAL LEU ILE ILE ASN THR GLY ASP GLY SER TYR ILE SEQRES 15 A 191 SER ARG GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *89(H2 O) HELIX 1 AA1 GLU A 100 TYR A 104 5 5 SHEET 1 AA1 5 ILE A 49 PHE A 54 0 SHEET 2 AA1 5 PHE A 36 ASN A 43 -1 N SER A 39 O LYS A 52 SHEET 3 AA1 5 ALA A 18 VAL A 28 -1 N VAL A 28 O PHE A 36 SHEET 4 AA1 5 THR A 12 VAL A 15 -1 N ILE A 13 O TRP A 20 SHEET 5 AA1 5 GLU A 61 PRO A 62 -1 O GLU A 61 N SER A 14 SHEET 1 AA2 5 GLN A 90 SER A 94 0 SHEET 2 AA2 5 ASN A 79 ASP A 84 -1 N HIS A 80 O LEU A 93 SHEET 3 AA2 5 GLU A 66 ASP A 76 -1 N ASP A 76 O ASN A 79 SHEET 4 AA2 5 GLU A 110 TYR A 116 -1 O THR A 115 N GLU A 66 SHEET 5 AA2 5 GLU A 119 GLU A 124 -1 O GLU A 124 N GLN A 112 SHEET 1 AA3 5 THR A 159 PRO A 163 0 SHEET 2 AA3 5 THR A 149 VAL A 154 -1 N LYS A 150 O VAL A 162 SHEET 3 AA3 5 THR A 128 GLU A 135 -1 N GLU A 135 O THR A 153 SHEET 4 AA3 5 VAL A 171 ASN A 175 -1 O LEU A 172 N LEU A 131 SHEET 5 AA3 5 TYR A 181 ARG A 184 -1 O SER A 183 N ILE A 173 CRYST1 30.266 43.460 126.343 90.00 90.00 90.00 P 21 21 21 4 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 0.033040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007915 0.00000