HEADER TRANSPORT PROTEIN 09-SEP-11 3TQL TITLE STRUCTURE OF THE AMINO ACID ABC TRANSPORTER, PERIPLASMIC AMINO ACID- TITLE 2 BINDING PROTEIN FROM COXIELLA BURNETII. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGININE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COXIELLA BURNETII; SOURCE 3 ORGANISM_TAXID: 777; SOURCE 4 STRAIN: RSA493; SOURCE 5 GENE: CBU_0482; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS TRANSPORT AND BINDING PROTEINS, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.RUDOLPH,J.CHEUNG,M.C.FRANKLIN,M.CASSIDY,E.GARY,F.BURSHTEYN,J.LOVE REVDAT 4 06-NOV-24 3TQL 1 REMARK LINK REVDAT 3 20-JAN-16 3TQL 1 JRNL REVDAT 2 24-JUN-15 3TQL 1 AUTHOR JRNL REVDAT 1 05-OCT-11 3TQL 0 JRNL AUTH M.C.FRANKLIN,J.CHEUNG,M.J.RUDOLPH,F.BURSHTEYN,M.CASSIDY, JRNL AUTH 2 E.GARY,B.HILLERICH,Z.K.YAO,P.R.CARLIER,M.TOTROV,J.D.LOVE JRNL TITL STRUCTURAL GENOMICS FOR DRUG DESIGN AGAINST THE PATHOGEN JRNL TITL 2 COXIELLA BURNETII. JRNL REF PROTEINS V. 83 2124 2015 JRNL REFN ISSN 0887-3585 JRNL PMID 26033498 JRNL DOI 10.1002/PROT.24841 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 35279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1769 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 43.7109 - 3.4341 1.00 3686 210 0.1602 0.1823 REMARK 3 2 3.4341 - 2.7259 0.94 3336 174 0.1620 0.2084 REMARK 3 3 2.7259 - 2.3813 0.97 3410 176 0.1630 0.2181 REMARK 3 4 2.3813 - 2.1636 0.88 3104 147 0.1410 0.2145 REMARK 3 5 2.1636 - 2.0085 0.99 3435 179 0.1492 0.2065 REMARK 3 6 2.0085 - 1.8901 0.90 3109 161 0.1889 0.2524 REMARK 3 7 1.8901 - 1.7954 0.96 3296 178 0.1722 0.2599 REMARK 3 8 1.7954 - 1.7173 0.99 3427 182 0.1688 0.2674 REMARK 3 9 1.7173 - 1.6512 1.00 3426 181 0.1536 0.2342 REMARK 3 10 1.6512 - 1.5942 0.96 3281 181 0.1751 0.2634 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 : 0.35 REMARK 3 B_SOL : 40.35 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.62110 REMARK 3 B22 (A**2) : -1.88070 REMARK 3 B33 (A**2) : 0.25960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1866 REMARK 3 ANGLE : 1.077 2535 REMARK 3 CHIRALITY : 0.077 286 REMARK 3 PLANARITY : 0.005 329 REMARK 3 DIHEDRAL : 12.842 690 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 3TQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35438 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.594 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 100 MM HEPES, PH 7.5, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.21050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.69450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.69450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.21050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.22500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 PRO A 59 REMARK 465 SER A 60 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 OE1 GLN A 77 O HOH A 346 2.19 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 ASP A 41 -60.93 22.10 REMARK 500 THR A 50 32.43 -148.42 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 ARG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 2 DBREF 3TQL A 40 266 UNP Q83E49 Q83E49_COXBU 40 266 SEQRES 1 A 227 THR ASP THR ILE LYS PHE ALA THR GLU ALA THR TYR PRO SEQRES 2 A 227 PRO TYR VAL TYR MSE GLY PRO SER GLY GLN VAL GLU GLY SEQRES 3 A 227 PHE GLY ALA ASP ILE VAL LYS ALA VAL CYS LYS GLN MSE SEQRES 4 A 227 GLN ALA VAL CYS THR ILE SER ASN GLN PRO TRP ASP SER SEQRES 5 A 227 LEU ILE PRO SER LEU LYS LEU GLY LYS PHE ASP ALA LEU SEQRES 6 A 227 PHE GLY GLY MSE ASN ILE THR THR ALA ARG GLN LYS GLU SEQRES 7 A 227 VAL ASP PHE THR ASP PRO TYR TYR THR ASN SER VAL SER SEQRES 8 A 227 PHE ILE ALA ASP LYS ASN THR PRO LEU THR LEU SER LYS SEQRES 9 A 227 GLN GLY LEU LYS GLY LYS ILE ILE GLY VAL GLN GLY GLY SEQRES 10 A 227 THR THR PHE ASP SER TYR LEU GLN ASP SER PHE GLY ASN SEQRES 11 A 227 SER ILE THR ILE GLN ARG TYR PRO SER GLU GLU ASP ALA SEQRES 12 A 227 LEU MSE ASP LEU THR SER GLY ARG VAL ASP ALA VAL VAL SEQRES 13 A 227 GLY ASP THR PRO LEU ILE LYS GLN TRP LEU LYS GLN ASN SEQRES 14 A 227 GLY ARG ARG GLU TYR VAL LEU ILE GLY LYS PRO VAL ASN SEQRES 15 A 227 ASP PRO ASN TYR PHE GLY LYS GLY VAL GLY ILE ALA VAL SEQRES 16 A 227 LYS LYS GLY ASN GLN ALA LEU LEU LEU LYS LEU ASN LYS SEQRES 17 A 227 ALA LEU ALA ALA ILE LYS ALA ASN GLY VAL TYR ALA ALA SEQRES 18 A 227 ILE VAL GLN LYS TYR PHE MODRES 3TQL MSE A 57 MET SELENOMETHIONINE MODRES 3TQL MSE A 78 MET SELENOMETHIONINE MODRES 3TQL MSE A 108 MET SELENOMETHIONINE MODRES 3TQL MSE A 184 MET SELENOMETHIONINE HET MSE A 57 8 HET MSE A 78 8 HET MSE A 108 16 HET MSE A 184 8 HET ARG A 1 12 HET IMD A 2 5 HETNAM MSE SELENOMETHIONINE HETNAM ARG ARGININE HETNAM IMD IMIDAZOLE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 ARG C6 H15 N4 O2 1+ FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 HOH *337(H2 O) HELIX 1 1 GLY A 65 MSE A 78 1 14 HELIX 2 2 PRO A 88 ASP A 90 5 3 HELIX 3 3 SER A 91 LEU A 98 1 8 HELIX 4 4 ALA A 113 LYS A 116 5 4 HELIX 5 5 THR A 157 GLY A 168 1 12 HELIX 6 6 ASN A 169 ILE A 171 5 3 HELIX 7 7 SER A 178 THR A 187 1 10 HELIX 8 8 ASP A 197 ASN A 208 1 12 HELIX 9 9 ASP A 222 PHE A 226 5 5 HELIX 10 10 ASN A 238 ASN A 255 1 18 HELIX 11 11 GLY A 256 PHE A 266 1 11 SHEET 1 A 5 VAL A 81 ASN A 86 0 SHEET 2 A 5 THR A 42 THR A 47 1 N PHE A 45 O SER A 85 SHEET 3 A 5 ALA A 103 LEU A 104 1 O ALA A 103 N ALA A 46 SHEET 4 A 5 ALA A 233 LYS A 235 -1 O ALA A 233 N LEU A 104 SHEET 5 A 5 VAL A 118 PHE A 120 -1 N ASP A 119 O VAL A 234 SHEET 1 B 2 TYR A 56 MSE A 57 0 SHEET 2 B 2 VAL A 63 GLU A 64 -1 O GLU A 64 N TYR A 56 SHEET 1 C 5 THR A 172 TYR A 176 0 SHEET 2 C 5 ILE A 150 GLN A 154 1 N ILE A 151 O THR A 172 SHEET 3 C 5 ALA A 193 VAL A 195 1 O ALA A 193 N GLY A 152 SHEET 4 C 5 SER A 128 ASP A 134 -1 N ILE A 132 O VAL A 194 SHEET 5 C 5 TYR A 213 PRO A 219 -1 O ILE A 216 N PHE A 131 SSBOND 1 CYS A 75 CYS A 82 1555 1555 2.07 LINK C TYR A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N GLY A 58 1555 1555 1.33 LINK C GLN A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N GLN A 79 1555 1555 1.32 LINK C GLY A 107 N AMSE A 108 1555 1555 1.33 LINK C GLY A 107 N BMSE A 108 1555 1555 1.33 LINK C AMSE A 108 N ASN A 109 1555 1555 1.33 LINK C BMSE A 108 N ASN A 109 1555 1555 1.34 LINK C LEU A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N ASP A 185 1555 1555 1.33 CISPEP 1 PRO A 52 PRO A 53 0 4.84 SITE 1 AC1 12 THR A 47 GLU A 48 THR A 50 TYR A 51 SITE 2 AC1 12 VAL A 55 TRP A 89 GLY A 106 GLY A 107 SITE 3 AC1 12 ASN A 109 ARG A 114 SER A 130 HOH A 366 SITE 1 AC2 1 VAL A 129 CRYST1 46.421 66.450 87.389 90.00 90.00 90.00 P 21 21 21 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 0.021542 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011443 0.00000