HEADER TRANSCRIPTION 05-OCT-18 6HU8 TITLE APO FORM OF THE COMPETENCE REGULATOR COMR FROM STREPTOCOCCUS TITLE 2 VESTIBULARIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR COMR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C-TERMINAL STREP-TAG SEQUENCE: GAGWSHPQFEK SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS VESTIBULARIS F0396; SOURCE 3 ORGANISM_TAXID: 904306; SOURCE 4 GENE: HMPREF9192_0126; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS RNPP FAMILY TPR DOMAIN HTH DOMAIN BACTERIAL SIGNALING PEPTIDE KEYWDS 2 BINDING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.NESSLER,J.THUILLIER,L.LEDESMA,P.HOLS REVDAT 4 24-JAN-24 6HU8 1 REMARK REVDAT 3 22-APR-20 6HU8 1 JRNL REVDAT 2 01-APR-20 6HU8 1 JRNL REVDAT 1 23-OCT-19 6HU8 0 JRNL AUTH L.LEDESMA-GARCIA,J.THUILLIER,A.GUZMAN-ESPINOLA,I.ENSINCK, JRNL AUTH 2 I.LI DE LA SIERRA-GALLAY,N.LAZAR,M.AUMONT-NICAISE, JRNL AUTH 3 J.MIGNOLET,P.SOUMILLION,S.NESSLER,P.HOLS JRNL TITL MOLECULAR DISSECTION OF PHEROMONE SELECTIVITY IN THE JRNL TITL 2 COMPETENCE SIGNALING SYSTEM COMRS OF STREPTOCOCCI. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 7745 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32198205 JRNL DOI 10.1073/PNAS.1916085117 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 26903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 36.8077 - 4.0781 1.00 2676 141 0.1566 0.1789 REMARK 3 2 4.0781 - 3.2375 1.00 2583 136 0.1921 0.2215 REMARK 3 3 3.2375 - 2.8284 1.00 2606 137 0.2302 0.2692 REMARK 3 4 2.8284 - 2.5699 1.00 2554 135 0.2374 0.2707 REMARK 3 5 2.5699 - 2.3857 1.00 2563 135 0.2361 0.2743 REMARK 3 6 2.3857 - 2.2451 1.00 2535 134 0.2460 0.2860 REMARK 3 7 2.2451 - 2.1327 1.00 2559 135 0.2525 0.2945 REMARK 3 8 2.1327 - 2.0399 1.00 2537 133 0.2956 0.3640 REMARK 3 9 2.0399 - 1.9613 0.99 2577 136 0.3430 0.4013 REMARK 3 10 1.9613 - 1.8937 0.94 2366 125 0.3670 0.3715 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.53 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 : 0.008 2508 REMARK 3 ANGLE : 1.000 3371 REMARK 3 CHIRALITY : 0.039 376 REMARK 3 PLANARITY : 0.004 428 REMARK 3 DIHEDRAL : 15.263 976 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 6HU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.894 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.660 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.050 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: 5JUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.15 M DL-MALIC ACID, 20 REMARK 280 MG/ML PROTEIN CONCENTRATION, PH 7, VAPOR DIFFUSION, TEMPERATURE REMARK 280 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.03500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.03500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.14500 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 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: 15500 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 1 REMARK 465 ALA A 301 REMARK 465 GLY A 302 REMARK 465 TRP A 303 REMARK 465 SER A 304 REMARK 465 HIS A 305 REMARK 465 PRO A 306 REMARK 465 GLN A 307 REMARK 465 PHE A 308 REMARK 465 GLU A 309 REMARK 465 LYS A 310 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 27 -124.56 47.54 REMARK 500 ASP A 68 -112.60 52.84 REMARK 500 ASP A 199 97.81 -173.72 REMARK 500 SER A 222 71.23 -113.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 6HU8 A 1 299 UNP E3CNF6 E3CNF6_STRVE 1 299 SEQADV 6HU8 GLY A 300 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 ALA A 301 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 GLY A 302 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 TRP A 303 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 SER A 304 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 HIS A 305 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 PRO A 306 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 GLN A 307 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 PHE A 308 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 GLU A 309 UNP E3CNF6 EXPRESSION TAG SEQADV 6HU8 LYS A 310 UNP E3CNF6 EXPRESSION TAG SEQRES 1 A 310 MET SER ILE LYS ASP SER ILE GLY LEU ARG ILE LYS THR SEQRES 2 A 310 GLU ARG GLU CYS GLN GLN MET SER ARG GLU VAL LEU CYS SEQRES 3 A 310 LEU ASP GLY ALA GLU LEU THR VAL ARG GLN LEU ILE ARG SEQRES 4 A 310 ILE GLU LYS GLY GLU SER LEU PRO SER LEU ASP LYS LEU SEQRES 5 A 310 SER TYR ILE ALA LYS ARG LEU GLY LYS SER MET ALA ASP SEQRES 6 A 310 LEU LEU ASP HIS ASP ARG ILE GLU ILE PRO ASP THR TYR SEQRES 7 A 310 TYR GLU MET LYS ASN ARG LEU ILE LYS PHE PRO THR TYR SEQRES 8 A 310 GLY ASP LYS GLU ARG VAL LYS GLN LYS LEU ASP LEU ILE SEQRES 9 A 310 GLU ASP VAL TYR ASN GLN PHE PHE ASP ILE LEU PRO GLU SEQRES 10 A 310 GLU GLU LEU LEU THR LEU ASP ILE LEU GLU ASN ILE LEU SEQRES 11 A 310 SER PHE THR SER TRP GLU GLU ARG PRO LYS VAL GLU GLU SEQRES 12 A 310 ILE TYR GLU ASP LEU PHE GLU GLN VAL LYS ARG LYS LYS SEQRES 13 A 310 LYS PHE SER THR ASN ASP LEU LEU VAL ILE ASP TYR TYR SEQRES 14 A 310 PHE TYR HIS LEU TYR GLY ARG LYS GLN TYR ASP LYS LYS SEQRES 15 A 310 ILE PHE ASP ARG ILE VAL ASP ARG VAL LEU LYS GLN ASN SEQRES 16 A 310 ILE PRO THR ASP ASP ALA TYR ASN ILE ALA LEU PHE ASN SEQRES 17 A 310 ASP LEU MET ALA ILE ALA GLY LEU LYS ILE SER LEU GLU SEQRES 18 A 310 SER PHE LYS ASP PHE LEU THR VAL ILE ASP LYS LEU LEU SEQRES 19 A 310 ALA VAL ILE GLU LYS SER GLN PHE HIS SER TYR LYS PRO SEQRES 20 A 310 GLY VAL TYR ILE LEU GLU ALA LYS TYR GLU LEU ILE HIS SEQRES 21 A 310 ASN GLY ASN LYS LYS LYS ALA THR GLU ASN TYR ASP LYS SEQRES 22 A 310 ALA ILE MET PHE ALA SER VAL LEU GLU ASP SER VAL LEU SEQRES 23 A 310 GLU GLU LYS THR ARG ALA GLU LYS ALA ALA ASP GLY LEU SEQRES 24 A 310 GLY ALA GLY TRP SER HIS PRO GLN PHE GLU LYS FORMUL 2 HOH *56(H2 O) HELIX 1 AA1 SER A 2 GLN A 18 1 17 HELIX 2 AA2 SER A 21 LEU A 27 1 7 HELIX 3 AA3 THR A 33 LYS A 42 1 10 HELIX 4 AA4 SER A 48 GLY A 60 1 13 HELIX 5 AA5 SER A 62 ASP A 68 1 7 HELIX 6 AA6 PRO A 75 PHE A 88 1 14 HELIX 7 AA7 ASP A 93 PHE A 112 1 20 HELIX 8 AA8 ASP A 113 LEU A 115 5 3 HELIX 9 AA9 PRO A 116 PHE A 132 1 17 HELIX 10 AB1 SER A 134 GLU A 137 5 4 HELIX 11 AB2 ARG A 138 LYS A 153 1 16 HELIX 12 AB3 SER A 159 TYR A 174 1 16 HELIX 13 AB4 ASP A 180 LYS A 193 1 14 HELIX 14 AB5 ASP A 199 LEU A 220 1 22 HELIX 15 AB6 ASP A 225 GLN A 241 1 17 HELIX 16 AB7 PHE A 242 SER A 244 5 3 HELIX 17 AB8 TYR A 245 GLY A 262 1 18 HELIX 18 AB9 ASN A 263 VAL A 280 1 18 HELIX 19 AC1 SER A 284 ASP A 297 1 14 CRYST1 110.070 38.290 87.620 90.00 113.20 90.00 C 1 2 1 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 0.009085 0.000000 0.003894 0.00000 SCALE2 0.000000 0.026116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012417 0.00000