HEADER TRANSCRIPTION 16-JAN-23 8C7O TITLE UNLIGANDED TRANSCRIPTIONAL PLEIOTROPIC REPRESSOR CODY FROM TITLE 2 STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLOBAL TRANSCRIPTIONAL REGULATOR CODY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN USA300); SOURCE 3 ORGANISM_TAXID: 367830; SOURCE 4 GENE: CODY, SAHV_1245; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTP SENSING, PLEIOTROPIC TRANSCRIPTION REGULATOR, DNA COMPLEX, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.HAINZL,A.E.SAUER-ERIKSSON REVDAT 4 15-NOV-23 8C7O 1 SOURCE REVDAT 3 23-AUG-23 8C7O 1 JRNL REVDAT 2 05-JUL-23 8C7O 1 JRNL REVDAT 1 28-JUN-23 8C7O 0 JRNL AUTH T.HAINZL,M.BONDE,F.ALMQVIST,J.JOHANSSON,A.E.SAUER-ERIKSSON JRNL TITL STRUCTURAL INSIGHTS INTO CODY ACTIVATION AND DNA JRNL TITL 2 RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 51 7631 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37326020 JRNL DOI 10.1093/NAR/GKAD512 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 33428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 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 1 2.1200 - 2.0500 1.00 3376 0 0.3430 0.4060 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) : 37.50 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8C7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292127966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33429 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 46.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN, 270 MICROM IN 20 MM TRIS-CL REMARK 280 PH 8, 200 MM NACL, 1 MM DTT WELL, 200 MM AMMONIUMSULPHATE, 100 REMARK 280 MM NAAC PH4.6, 22-25% PEG4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 81.92600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A -1 REMARK 465 ALA A 0 REMARK 465 LYS A 257 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 LYS B 257 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 56 30.37 -89.34 REMARK 500 VAL B 36 65.78 60.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 8C7O A 1 257 UNP A7X1N2 CODY_STAA1 1 257 DBREF 8C7O B 1 257 UNP A7X1N2 CODY_STAA1 1 257 SEQADV 8C7O GLY A -1 UNP A7X1N2 EXPRESSION TAG SEQADV 8C7O ALA A 0 UNP A7X1N2 EXPRESSION TAG SEQADV 8C7O GLY B -1 UNP A7X1N2 EXPRESSION TAG SEQADV 8C7O ALA B 0 UNP A7X1N2 EXPRESSION TAG SEQRES 1 A 259 GLY ALA MET SER LEU LEU SER LYS THR ARG GLU LEU ASN SEQRES 2 A 259 THR LEU LEU GLN LYS HIS LYS GLY ILE ALA VAL ASP PHE SEQRES 3 A 259 LYS ASP VAL ALA GLN THR ILE SER SER VAL THR VAL THR SEQRES 4 A 259 ASN VAL PHE ILE VAL SER ARG ARG GLY LYS ILE LEU GLY SEQRES 5 A 259 SER SER LEU ASN GLU LEU LEU LYS SER GLN ARG ILE ILE SEQRES 6 A 259 GLN MET LEU GLU GLU ARG HIS ILE PRO SER GLU TYR THR SEQRES 7 A 259 GLU ARG LEU MET GLU VAL LYS GLN THR GLU SER ASN ILE SEQRES 8 A 259 ASP ILE ASP ASN VAL LEU THR VAL PHE PRO PRO GLU ASN SEQRES 9 A 259 ARG GLU LEU PHE ILE ASP SER ARG THR THR ILE PHE PRO SEQRES 10 A 259 ILE LEU GLY GLY GLY GLU ARG LEU GLY THR LEU VAL LEU SEQRES 11 A 259 GLY ARG VAL HIS ASP ASP PHE ASN GLU ASN ASP LEU VAL SEQRES 12 A 259 LEU GLY GLU TYR ALA ALA THR VAL ILE GLY MET GLU ILE SEQRES 13 A 259 LEU ARG GLU LYS HIS SER GLU VAL GLU LYS GLU ALA ARG SEQRES 14 A 259 ASP LYS ALA ALA ILE THR MET ALA ILE ASN SER LEU SER SEQRES 15 A 259 TYR SER GLU LYS GLU ALA ILE GLU HIS ILE PHE GLU GLU SEQRES 16 A 259 LEU GLY GLY THR GLU GLY LEU LEU ILE ALA SER LYS VAL SEQRES 17 A 259 ALA ASP ARG VAL GLY ILE THR ARG SER VAL ILE VAL ASN SEQRES 18 A 259 ALA LEU ARG LYS LEU GLU SER ALA GLY VAL ILE GLU SER SEQRES 19 A 259 ARG SER LEU GLY MET LYS GLY THR PHE ILE LYS VAL LYS SEQRES 20 A 259 LYS GLU LYS PHE LEU ASP GLU LEU GLU LYS SER LYS SEQRES 1 B 259 GLY ALA MET SER LEU LEU SER LYS THR ARG GLU LEU ASN SEQRES 2 B 259 THR LEU LEU GLN LYS HIS LYS GLY ILE ALA VAL ASP PHE SEQRES 3 B 259 LYS ASP VAL ALA GLN THR ILE SER SER VAL THR VAL THR SEQRES 4 B 259 ASN VAL PHE ILE VAL SER ARG ARG GLY LYS ILE LEU GLY SEQRES 5 B 259 SER SER LEU ASN GLU LEU LEU LYS SER GLN ARG ILE ILE SEQRES 6 B 259 GLN MET LEU GLU GLU ARG HIS ILE PRO SER GLU TYR THR SEQRES 7 B 259 GLU ARG LEU MET GLU VAL LYS GLN THR GLU SER ASN ILE SEQRES 8 B 259 ASP ILE ASP ASN VAL LEU THR VAL PHE PRO PRO GLU ASN SEQRES 9 B 259 ARG GLU LEU PHE ILE ASP SER ARG THR THR ILE PHE PRO SEQRES 10 B 259 ILE LEU GLY GLY GLY GLU ARG LEU GLY THR LEU VAL LEU SEQRES 11 B 259 GLY ARG VAL HIS ASP ASP PHE ASN GLU ASN ASP LEU VAL SEQRES 12 B 259 LEU GLY GLU TYR ALA ALA THR VAL ILE GLY MET GLU ILE SEQRES 13 B 259 LEU ARG GLU LYS HIS SER GLU VAL GLU LYS GLU ALA ARG SEQRES 14 B 259 ASP LYS ALA ALA ILE THR MET ALA ILE ASN SER LEU SER SEQRES 15 B 259 TYR SER GLU LYS GLU ALA ILE GLU HIS ILE PHE GLU GLU SEQRES 16 B 259 LEU GLY GLY THR GLU GLY LEU LEU ILE ALA SER LYS VAL SEQRES 17 B 259 ALA ASP ARG VAL GLY ILE THR ARG SER VAL ILE VAL ASN SEQRES 18 B 259 ALA LEU ARG LYS LEU GLU SER ALA GLY VAL ILE GLU SER SEQRES 19 B 259 ARG SER LEU GLY MET LYS GLY THR PHE ILE LYS VAL LYS SEQRES 20 B 259 LYS GLU LYS PHE LEU ASP GLU LEU GLU LYS SER LYS HET SO4 A 301 5 HET SO4 A 302 10 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HET ACT A 307 4 HET SO4 A 308 5 HET SO4 B 301 5 HET SO4 B 302 5 HET SO4 B 303 5 HET SO4 B 304 5 HET SO4 B 305 5 HET SO4 B 306 5 HET SO4 B 307 5 HET SO4 B 308 5 HET SO4 B 309 5 HET SO4 B 310 5 HET SO4 B 311 5 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION FORMUL 3 SO4 18(O4 S 2-) FORMUL 9 ACT C2 H3 O2 1- FORMUL 22 HOH *98(H2 O) HELIX 1 AA1 SER A 2 GLN A 15 1 14 HELIX 2 AA2 ASP A 23 VAL A 36 1 14 HELIX 3 AA3 SER A 59 ARG A 69 1 11 HELIX 4 AA4 PRO A 72 MET A 80 1 9 HELIX 5 AA5 ASN A 136 LEU A 179 1 44 HELIX 6 AA6 SER A 180 GLY A 195 1 16 HELIX 7 AA7 ILE A 202 GLY A 211 1 10 HELIX 8 AA8 THR A 213 ALA A 227 1 15 HELIX 9 AA9 LYS A 248 SER A 256 1 9 HELIX 10 AB1 SER B 2 GLN B 15 1 14 HELIX 11 AB2 ASP B 23 VAL B 36 1 14 HELIX 12 AB3 SER B 59 ARG B 69 1 11 HELIX 13 AB4 PRO B 72 LEU B 79 1 8 HELIX 14 AB5 MET B 80 VAL B 82 5 3 HELIX 15 AB6 ASN B 136 LEU B 179 1 44 HELIX 16 AB7 SER B 180 GLY B 195 1 16 HELIX 17 AB8 ILE B 202 GLY B 211 1 10 HELIX 18 AB9 THR B 213 ALA B 227 1 15 HELIX 19 AC1 LYS B 248 SER B 256 1 9 SHEET 1 AA1 5 ILE A 48 SER A 52 0 SHEET 2 AA1 5 ASN A 38 SER A 43 -1 N ILE A 41 O GLY A 50 SHEET 3 AA1 5 GLU A 121 ARG A 130 -1 O THR A 125 N VAL A 42 SHEET 4 AA1 5 ARG A 110 GLY A 118 -1 N PHE A 114 O LEU A 126 SHEET 5 AA1 5 GLU A 86 ILE A 89 -1 N ILE A 89 O THR A 111 SHEET 1 AA2 3 GLU A 198 LEU A 201 0 SHEET 2 AA2 3 THR A 240 VAL A 244 -1 O THR A 240 N LEU A 201 SHEET 3 AA2 3 ILE A 230 SER A 234 -1 N ARG A 233 O PHE A 241 SHEET 1 AA3 5 ILE B 48 SER B 52 0 SHEET 2 AA3 5 ASN B 38 SER B 43 -1 N ILE B 41 O GLY B 50 SHEET 3 AA3 5 GLU B 121 ARG B 130 -1 O THR B 125 N VAL B 42 SHEET 4 AA3 5 ARG B 110 GLY B 118 -1 N ILE B 116 O LEU B 123 SHEET 5 AA3 5 GLU B 86 ILE B 89 -1 N ILE B 89 O THR B 111 SHEET 1 AA4 3 GLU B 198 LEU B 201 0 SHEET 2 AA4 3 THR B 240 VAL B 244 -1 O THR B 240 N LEU B 201 SHEET 3 AA4 3 ILE B 230 SER B 234 -1 N ARG B 233 O PHE B 241 CRYST1 35.803 163.852 46.868 90.00 93.80 90.00 P 1 21 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 0.027931 0.000000 0.001857 0.00000 SCALE2 0.000000 0.006103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021384 0.00000