HEADER PROTEIN BINDING 06-FEB-18 6CCD TITLE THE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RV1747 FHA-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABC TRANSPORTER ATP-BINDING/PERMEASE PROTEIN RV1747; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TANDEM FHA REGULATORY MODULE (UNP RESIDUES 3-113); COMPND 5 SYNONYM: RV1747 FHA-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: RV1747; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS FHA DOMAIN, PHOSPHO-THREONINE BINDING DOMAIN, PHOSPHO-PEPTIDE BINDING KEYWDS 2 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.M.GAY,C.L.GEE,T.ALBER REVDAT 5 13-MAR-24 6CCD 1 REMARK REVDAT 4 01-JAN-20 6CCD 1 REMARK REVDAT 3 20-FEB-19 6CCD 1 REMARK REVDAT 2 18-JUL-18 6CCD 1 JRNL REVDAT 1 20-JUN-18 6CCD 0 JRNL AUTH F.HEINKEL,L.SHEN,M.RICHARD-GREENBLATT,M.OKON,J.M.BUI, JRNL AUTH 2 C.L.GEE,L.M.GAY,T.ALBER,Y.AV-GAY,J.GSPONER,L.P.MCINTOSH JRNL TITL BIOPHYSICAL CHARACTERIZATION OF THE TANDEM FHA DOMAIN JRNL TITL 2 REGULATORY MODULE FROM THE MYCOBACTERIUM TUBERCULOSIS ABC JRNL TITL 3 TRANSPORTER RV1747. JRNL REF STRUCTURE V. 26 972 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29861345 JRNL DOI 10.1016/J.STR.2018.04.018 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 11495 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1045 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 51.0484 - 3.4432 1.00 3376 163 0.1610 0.1939 REMARK 3 2 3.4432 - 2.7330 1.00 3334 186 0.1603 0.1828 REMARK 3 3 2.7330 - 2.3875 1.00 3325 197 0.1682 0.2429 REMARK 3 4 2.3875 - 2.1692 0.99 3358 148 0.1617 0.1906 REMARK 3 5 2.1692 - 2.0138 0.93 3117 154 0.1711 0.2036 REMARK 3 6 2.0138 - 1.8950 0.66 2212 110 0.2158 0.2710 REMARK 3 7 1.8950 - 1.8001 0.48 1627 87 0.2649 0.3220 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.820 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 : 0.007 832 REMARK 3 ANGLE : 1.134 1136 REMARK 3 CHIRALITY : 0.049 121 REMARK 3 PLANARITY : 0.005 153 REMARK 3 DIHEDRAL : 13.975 307 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 6CCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.47 (08-JUL-2014) REMARK 200 DATA SCALING SOFTWARE : AIMLESS VERSION 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 68.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 68.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.02400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 69.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: SINGLE, ROD-SHAPED CRYSTALS OF APPROXIMATELY 0.4 MM LENGTH REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 18 MG/ML PROTEIN (IN 50 MM SODIUM REMARK 280 CHLORIDE, 25 MM HEPES, 0.5 MM TCEP, PH 7.8), 1.8 M AMMONIUM REMARK 280 SULFATE, 100 MM CITRATE BUFFER, PH 5.5, WITH 10% SILICON, 90% REMARK 280 PARAFFIN SOLUTION AS OVERLAY, MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.75467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.87733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.87733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.75467 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: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 3 REMARK 465 SER A 4 REMARK 465 GLN A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 HIS A 106 REMARK 465 ARG A 107 REMARK 465 GLY A 108 REMARK 465 SER A 109 REMARK 465 ALA A 110 REMARK 465 GLY A 111 REMARK 465 ARG A 112 REMARK 465 PRO A 113 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 337 O HOH A 383 2.13 REMARK 500 O HOH A 345 O HOH A 368 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 325 O HOH A 338 2564 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 17 56.23 35.22 REMARK 500 ASN A 65 53.41 -91.66 REMARK 500 ASP A 85 -56.40 -135.43 REMARK 500 ASN A 93 163.91 178.70 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 DBREF 6CCD A 3 113 UNP O65934 ABC1_MYCTU 3 113 SEQRES 1 A 111 MET SER GLN PRO ALA ALA PRO PRO VAL LEU THR VAL ARG SEQRES 2 A 111 TYR GLU GLY SER GLU ARG THR PHE ALA ALA GLY HIS ASP SEQRES 3 A 111 VAL VAL VAL GLY ARG ASP LEU ARG ALA ASP VAL ARG VAL SEQRES 4 A 111 ALA HIS PRO LEU ILE SER ARG ALA HIS LEU LEU LEU ARG SEQRES 5 A 111 PHE ASP GLN GLY ARG TRP VAL ALA ILE ASP ASN GLY SER SEQRES 6 A 111 LEU ASN GLY LEU TYR LEU ASN ASN ARG ARG VAL PRO VAL SEQRES 7 A 111 VAL ASP ILE TYR ASP ALA GLN ARG VAL HIS ILE GLY ASN SEQRES 8 A 111 PRO ASP GLY PRO ALA LEU ASP PHE GLU VAL GLY ARG HIS SEQRES 9 A 111 ARG GLY SER ALA GLY ARG PRO HET SO4 A 201 5 HET SO4 A 202 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *100(H2 O) SHEET 1 AA1 6 SER A 19 PHE A 23 0 SHEET 2 AA1 6 LEU A 12 TYR A 16 -1 N TYR A 16 O SER A 19 SHEET 3 AA1 6 ALA A 98 VAL A 103 -1 O GLU A 102 N THR A 13 SHEET 4 AA1 6 ALA A 86 ILE A 91 -1 N GLN A 87 O PHE A 101 SHEET 5 AA1 6 LEU A 71 LEU A 73 -1 N TYR A 72 O HIS A 90 SHEET 6 AA1 6 ARG A 76 ARG A 77 -1 O ARG A 76 N LEU A 73 SHEET 1 AA2 5 VAL A 39 ARG A 40 0 SHEET 2 AA2 5 VAL A 29 GLY A 32 1 N GLY A 32 O VAL A 39 SHEET 3 AA2 5 LEU A 51 ASP A 56 -1 O LEU A 53 N VAL A 29 SHEET 4 AA2 5 ARG A 59 ASP A 64 -1 O ILE A 63 N LEU A 52 SHEET 5 AA2 5 VAL A 80 ILE A 83 -1 O ILE A 83 N TRP A 60 SITE 1 AC1 6 ARG A 33 SER A 47 ARG A 48 HOH A 302 SITE 2 AC1 6 HOH A 337 HOH A 360 SITE 1 AC2 4 HIS A 27 ASP A 28 HOH A 326 HOH A 335 CRYST1 58.922 58.922 68.632 90.00 90.00 120.00 P 32 2 1 6 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 0.016972 0.009799 0.000000 0.00000 SCALE2 0.000000 0.019597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014570 0.00000