HEADER TRANSLATION 16-APR-21 7O9I TITLE ESCHERICHIA COLI FFH IN COMPLEX WITH PPPGPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL RECOGNITION PARTICLE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FIFTY-FOUR HOMOLOG,FFH,P48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: FFH, B2610, JW5414; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS STRINGENT RESPONSE, TARGETING COMPLEX, SIGNAL RECOGNITION PARTICLE, KEYWDS 2 ALARMONES, STRESS, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR L.CZECH,C.-N.MAIS,G.BANGE REVDAT 4 31-JAN-24 7O9I 1 REMARK REVDAT 3 27-SEP-23 7O9I 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL ATOM REVDAT 2 09-MAR-22 7O9I 1 JRNL REVDAT 1 02-FEB-22 7O9I 0 JRNL AUTH L.CZECH,C.N.MAIS,H.KRATZAT,P.SARMAH,P.GIAMMARINARO, JRNL AUTH 2 S.A.FREIBERT,H.F.ESSER,J.MUSIAL,O.BERNINGHAUSEN,W.STEINCHEN, JRNL AUTH 3 R.BECKMANN,H.G.KOCH,G.BANGE JRNL TITL INHIBITION OF SRP-DEPENDENT PROTEIN SECRETION BY THE JRNL TITL 2 BACTERIAL ALARMONE (P)PPGPP. JRNL REF NAT COMMUN V. 13 1069 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35217658 JRNL DOI 10.1038/S41467-022-28675-0 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 11724 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 585 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 41.0500 - 3.9600 1.00 2831 149 0.2115 0.2414 REMARK 3 2 3.9500 - 3.1400 1.00 2806 147 0.2494 0.2868 REMARK 3 3 3.1400 - 2.7400 1.00 2775 147 0.2793 0.3344 REMARK 3 4 2.7400 - 2.4900 0.98 2727 142 0.2672 0.3698 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 2240 REMARK 3 ANGLE : 1.271 3041 REMARK 3 CHIRALITY : 0.071 362 REMARK 3 PLANARITY : 0.008 387 REMARK 3 DIHEDRAL : 20.644 326 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 7O9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292115298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976253 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11747 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 41.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3NG1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M CHES PH REMARK 280 9.5, 50% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.84000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.42000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.26000 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: 13670 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 MET A 0 REMARK 465 GLY A 1 REMARK 465 PHE A 2 REMARK 465 ASP A 3 REMARK 465 ASN A 4 REMARK 465 LEU A 5 REMARK 465 THR A 6 REMARK 465 ASP A 7 REMARK 465 ARG A 8 REMARK 465 LEU A 295 REMARK 465 GLY A 296 REMARK 465 MET A 297 REMARK 465 GLY A 298 REMARK 465 ASP A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 REMARK 465 HIS A 305 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 ARG A 11 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 22 CG CD1 CD2 REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 49 CG CD NE CZ NH1 NH2 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 GLU A 88 -59.04 72.60 REMARK 500 ALA A 97 -159.63 -92.73 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 0O2 A 401 DBREF 7O9I A 3 299 UNP P0AGD7 SRP54_ECOLI 3 299 SEQADV 7O9I MET A 0 UNP P0AGD7 INITIATING METHIONINE SEQADV 7O9I GLY A 1 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I PHE A 2 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 300 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 301 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 302 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 303 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 304 UNP P0AGD7 EXPRESSION TAG SEQADV 7O9I HIS A 305 UNP P0AGD7 EXPRESSION TAG SEQRES 1 A 306 MET GLY PHE ASP ASN LEU THR ASP ARG LEU SER ARG THR SEQRES 2 A 306 LEU ARG ASN ILE SER GLY ARG GLY ARG LEU THR GLU ASP SEQRES 3 A 306 ASN VAL LYS ASP THR LEU ARG GLU VAL ARG MET ALA LEU SEQRES 4 A 306 LEU GLU ALA ASP VAL ALA LEU PRO VAL VAL ARG GLU PHE SEQRES 5 A 306 ILE ASN ARG VAL LYS GLU LYS ALA VAL GLY HIS GLU VAL SEQRES 6 A 306 ASN LYS SER LEU THR PRO GLY GLN GLU PHE VAL LYS ILE SEQRES 7 A 306 VAL ARG ASN GLU LEU VAL ALA ALA MET GLY GLU GLU ASN SEQRES 8 A 306 GLN THR LEU ASN LEU ALA ALA GLN PRO PRO ALA VAL VAL SEQRES 9 A 306 LEU MET ALA GLY LEU GLN GLY ALA GLY LYS THR THR SER SEQRES 10 A 306 VAL GLY LYS LEU GLY LYS PHE LEU ARG GLU LYS HIS LYS SEQRES 11 A 306 LYS LYS VAL LEU VAL VAL SER ALA ASP VAL TYR ARG PRO SEQRES 12 A 306 ALA ALA ILE LYS GLN LEU GLU THR LEU ALA GLU GLN VAL SEQRES 13 A 306 GLY VAL ASP PHE PHE PRO SER ASP VAL GLY GLN LYS PRO SEQRES 14 A 306 VAL ASP ILE VAL ASN ALA ALA LEU LYS GLU ALA LYS LEU SEQRES 15 A 306 LYS PHE TYR ASP VAL LEU LEU VAL ASP THR ALA GLY ARG SEQRES 16 A 306 LEU HIS VAL ASP GLU ALA MET MET ASP GLU ILE LYS GLN SEQRES 17 A 306 VAL HIS ALA SER ILE ASN PRO VAL GLU THR LEU PHE VAL SEQRES 18 A 306 VAL ASP ALA MET THR GLY GLN ASP ALA ALA ASN THR ALA SEQRES 19 A 306 LYS ALA PHE ASN GLU ALA LEU PRO LEU THR GLY VAL VAL SEQRES 20 A 306 LEU THR LYS VAL ASP GLY ASP ALA ARG GLY GLY ALA ALA SEQRES 21 A 306 LEU SER ILE ARG HIS ILE THR GLY LYS PRO ILE LYS PHE SEQRES 22 A 306 LEU GLY VAL GLY GLU LYS THR GLU ALA LEU GLU PRO PHE SEQRES 23 A 306 HIS PRO ASP ARG ILE ALA SER ARG ILE LEU GLY MET GLY SEQRES 24 A 306 ASP HIS HIS HIS HIS HIS HIS HET 0O2 A 401 40 HETNAM 0O2 GUANOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) 3'- HETNAM 2 0O2 (TRIHYDROGEN DIPHOSPHATE) FORMUL 2 0O2 C10 H18 N5 O20 P5 FORMUL 3 HOH *14(H2 O) HELIX 1 AA1 LEU A 9 SER A 17 1 9 HELIX 2 AA2 GLU A 24 VAL A 43 1 20 HELIX 3 AA3 VAL A 47 GLU A 63 1 17 HELIX 4 AA4 VAL A 64 SER A 67 5 4 HELIX 5 AA5 THR A 69 MET A 86 1 18 HELIX 6 AA6 GLY A 112 LYS A 127 1 16 HELIX 7 AA7 ALA A 143 GLY A 156 1 14 HELIX 8 AA8 LYS A 167 LYS A 182 1 16 HELIX 9 AA9 ASP A 198 ASN A 213 1 16 HELIX 10 AB1 GLY A 226 LEU A 240 1 15 HELIX 11 AB2 LYS A 249 ASP A 253 5 5 HELIX 12 AB3 GLY A 257 GLY A 267 1 11 HELIX 13 AB4 HIS A 286 ILE A 294 1 9 SHEET 1 AA1 8 ASP A 158 PHE A 159 0 SHEET 2 AA1 8 VAL A 132 SER A 136 1 N VAL A 132 O ASP A 158 SHEET 3 AA1 8 VAL A 186 ASP A 190 1 O LEU A 188 N LEU A 133 SHEET 4 AA1 8 ALA A 101 ALA A 106 1 N ALA A 101 O LEU A 187 SHEET 5 AA1 8 GLU A 216 ASP A 222 1 O LEU A 218 N LEU A 104 SHEET 6 AA1 8 GLY A 244 THR A 248 1 O VAL A 246 N PHE A 219 SHEET 7 AA1 8 ILE A 270 GLY A 274 1 O GLY A 274 N LEU A 247 SHEET 8 AA1 8 LEU A 282 PRO A 284 -1 O GLU A 283 N LEU A 273 CISPEP 1 PRO A 99 PRO A 100 0 -1.26 SITE 1 AC1 18 LEU A 108 GLY A 110 ALA A 111 GLY A 112 SITE 2 AC1 18 LYS A 113 THR A 114 THR A 115 LYS A 119 SITE 3 AC1 18 ASP A 138 GLN A 147 ASP A 190 LYS A 249 SITE 4 AC1 18 ASP A 251 GLY A 274 VAL A 275 GLY A 276 SITE 5 AC1 18 GLU A 277 HOH A 503 CRYST1 58.060 58.060 101.680 90.00 90.00 90.00 P 41 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 0.017224 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009835 0.00000