HEADER SIGNALING PROTEIN 29-DEC-24 9HVJ TITLE LIGAND BINDING DOMAIN OF ROSEBURIA INTESTINALIS L1-82 URACIL TITLE 2 CHEMORECEPTOR (DCACHE) IN COMPLEX WITH URACIL AND ACETATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CACHE DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METHYL-ACCEPTING CHEMOTAXIS PROTEIN MCPC; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSEBURIA INTESTINALIS L1-82; SOURCE 3 ORGANISM_TAXID: 536231; SOURCE 4 GENE: MCPC_1, RIL182_00127, ROSINTL182_06964; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS KEYWDS CHEMORECEPTOR, DCACHE DOMAIN, URACIL, ACETATE, CHEMOTAXIS, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.JALOMO-KHAYROVA,G.BANGE REVDAT 1 12-MAR-25 9HVJ 0 JRNL AUTH W.XU,E.JALOMO-KHAYROVA,V.M.GUMEROV,P.A.ROSS,T.S.KOBEL, JRNL AUTH 2 D.SCHINDLER,G.BANGE,I.B.ZHULIN,V.SOURJIK JRNL TITL SPECIFICITIES OF CHEMOSENSORY RECEPTORS IN THE HUMAN GUT JRNL TITL 2 MICROBIOTA. JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL PMID 39990360 JRNL DOI 10.1101/2025.02.11.637667 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 48332 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2416 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 46.5400 - 3.7600 0.99 2755 144 0.1441 0.1504 REMARK 3 2 3.7600 - 2.9900 1.00 2726 144 0.1505 0.1592 REMARK 3 3 2.9900 - 2.6100 0.99 2709 143 0.1699 0.1795 REMARK 3 4 2.6100 - 2.3700 0.99 2721 143 0.1648 0.1866 REMARK 3 5 2.3700 - 2.2000 1.00 2696 142 0.1616 0.1688 REMARK 3 6 2.2000 - 2.0700 0.99 2728 143 0.1565 0.1820 REMARK 3 7 2.0700 - 1.9700 1.00 2717 143 0.1656 0.2031 REMARK 3 8 1.9700 - 1.8800 1.00 2726 144 0.1684 0.2050 REMARK 3 9 1.8800 - 1.8100 1.00 2694 141 0.1726 0.2091 REMARK 3 10 1.8100 - 1.7500 1.00 2687 142 0.1690 0.1948 REMARK 3 11 1.7500 - 1.6900 1.00 2711 143 0.1772 0.2082 REMARK 3 12 1.6900 - 1.6400 1.00 2715 143 0.1831 0.2060 REMARK 3 13 1.6400 - 1.6000 1.00 2711 142 0.1914 0.2373 REMARK 3 14 1.6000 - 1.5600 1.00 2709 143 0.2117 0.2594 REMARK 3 15 1.5600 - 1.5300 0.99 2678 141 0.2176 0.2427 REMARK 3 16 1.5300 - 1.4900 0.99 2726 143 0.2268 0.2401 REMARK 3 17 1.4900 - 1.4600 0.93 2507 132 0.2366 0.3011 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.853 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.83 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 2376 REMARK 3 ANGLE : 0.895 3243 REMARK 3 CHIRALITY : 0.086 360 REMARK 3 PLANARITY : 0.007 422 REMARK 3 DIHEDRAL : 5.327 337 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 9HVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.87313 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48349 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 46.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.16730 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.94190 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.310 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM FLUORIDE, 20% (W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, 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 46.54000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 12 REMARK 465 GLY A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 31 REMARK 465 MET A 32 REMARK 465 SER A 33 REMARK 465 THR A 34 REMARK 465 LYS A 305 REMARK 465 SER A 306 REMARK 465 ARG A 307 REMARK 465 GLN A 308 REMARK 465 LEU A 309 REMARK 465 ALA A 310 REMARK 465 LYS A 311 REMARK 465 GLN A 312 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 PHE A 221 -141.24 57.65 REMARK 500 SER A 223 16.70 -145.26 REMARK 500 ASP A 251 126.34 -170.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 9HVJ A 33 312 UNP C7GAN4 C7GAN4_9FIRM 33 312 SEQADV 9HVJ MET A 12 UNP C7GAN4 INITIATING METHIONINE SEQADV 9HVJ GLY A 13 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ SER A 14 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ SER A 15 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 16 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 17 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 18 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 19 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 20 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 21 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ SER A 22 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ SER A 23 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ GLY A 24 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ LEU A 25 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ VAL A 26 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ PRO A 27 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ ARG A 28 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ GLY A 29 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ SER A 30 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ HIS A 31 UNP C7GAN4 EXPRESSION TAG SEQADV 9HVJ MET A 32 UNP C7GAN4 EXPRESSION TAG SEQRES 1 A 301 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 301 LEU VAL PRO ARG GLY SER HIS MET SER THR SER TYR GLU SEQRES 3 A 301 ASP SER GLN GLN GLU MET GLN LEU LYS CYS VAL SER GLN SEQRES 4 A 301 SER ASP GLU LEU ASP THR MET MET GLN ASN VAL SER GLN SEQRES 5 A 301 SER VAL GLU MET VAL TYR SER ILE ALA VAL ALA LYS LEU SEQRES 6 A 301 GLU HIS ALA ALA SER PHE ARG THR SER LYS ASP TYR VAL SEQRES 7 A 301 ASP THR TYR THR LYS GLN MET LEU PRO ILE LEU MET GLN SEQRES 8 A 301 SER ALA GLN ASN THR LYS GLY ALA LEU THR ALA TYR ILE SEQRES 9 A 301 ARG TYR ASN PRO GLU PHE THR GLU PRO THR SER GLY LEU SEQRES 10 A 301 PHE LEU THR ARG ASP ASN SER ASP SER GLU PHE GLU SER SEQRES 11 A 301 VAL THR PRO THR ASP PHE SER MET TYR ASP PRO SER ASP SEQRES 12 A 301 VAL GLU HIS VAL GLY TRP TYR TYR ILE PRO VAL GLN ASN SEQRES 13 A 301 GLY LYS GLU THR TRP MET GLU PRO TYR LEU ASN SER ASN SEQRES 14 A 301 ILE GLY VAL TYR MET ILE SER TYR VAL ILE PRO ILE GLU SEQRES 15 A 301 VAL ASP GLY GLU SER ILE GLY ILE ILE GLY MET ASP ILE SEQRES 16 A 301 ASP PHE SER GLU PHE THR ASP THR ILE ASP SER LEU SER SEQRES 17 A 301 ILE PHE ASP SER GLY TYR GLY PHE LEU VAL ASN GLU SER SEQRES 18 A 301 GLY LYS VAL MET TYR HIS LYS ASP LEU GLU ILE GLY SER SEQRES 19 A 301 ASN LEU ALA ASP ALA ASP SER GLY LEU GLN SER VAL VAL SEQRES 20 A 301 ASP ALA LEU GLY ASN GLU GLN THR GLU GLU THR ALA VAL SEQRES 21 A 301 SER TYR THR TYR GLN GLY LYS ASP LYS VAL MET TYR TYR SEQRES 22 A 301 LYS THR LEU GLU ASN GLY MET LYS PHE VAL LEU THR ALA SEQRES 23 A 301 PRO LYS THR GLU LEU GLN GLU LYS SER ARG GLN LEU ALA SEQRES 24 A 301 LYS GLN HET URA A 401 8 HET ACT A 402 4 HET EDO A 403 4 HETNAM URA URACIL HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 URA C4 H4 N2 O2 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *265(H2 O) HELIX 1 AA1 TYR A 36 LEU A 76 1 41 HELIX 2 AA2 HIS A 78 ARG A 83 5 6 HELIX 3 AA3 SER A 85 ASN A 106 1 22 HELIX 4 AA4 ASP A 146 TYR A 150 5 5 HELIX 5 AA5 ASP A 154 GLY A 168 1 15 HELIX 6 AA6 PHE A 208 SER A 217 1 10 HELIX 7 AA7 ASN A 246 ALA A 250 5 5 HELIX 8 AA8 ASP A 251 GLY A 253 5 3 HELIX 9 AA9 LEU A 254 GLY A 262 1 9 HELIX 10 AB1 ASN A 263 GLU A 267 5 5 HELIX 11 AB2 LYS A 299 GLN A 303 1 5 SHEET 1 AA1 6 GLU A 140 VAL A 142 0 SHEET 2 AA1 6 LEU A 128 THR A 131 -1 N PHE A 129 O VAL A 142 SHEET 3 AA1 6 THR A 112 TYR A 117 -1 N ALA A 113 O LEU A 130 SHEET 4 AA1 6 GLU A 197 ASP A 207 -1 O ILE A 201 N ARG A 116 SHEET 5 AA1 6 VAL A 183 VAL A 194 -1 N ILE A 192 O GLY A 200 SHEET 6 AA1 6 THR A 171 ASN A 178 -1 N MET A 173 O SER A 187 SHEET 1 AA2 5 VAL A 235 TYR A 237 0 SHEET 2 AA2 5 TYR A 225 VAL A 229 -1 N LEU A 228 O TYR A 237 SHEET 3 AA2 5 LYS A 292 PRO A 298 -1 O LYS A 292 N VAL A 229 SHEET 4 AA2 5 LYS A 278 THR A 286 -1 N TYR A 283 O LEU A 295 SHEET 5 AA2 5 VAL A 271 TYR A 275 -1 N TYR A 273 O LYS A 280 CRYST1 35.000 93.080 44.380 90.00 92.19 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 0.028571 0.000000 0.001093 0.00000 SCALE2 0.000000 0.010743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022549 0.00000