HEADER TRANSPORT PROTEIN 24-JAN-15 4XTT TITLE STRUCTURAL STUDIES OF POTASSIUM TRANSPORT PROTEIN KTRA REGULATOR OF TITLE 2 CONDUCTANCE OF K+ (RCK) C DOMAIN IN COMPLEX WITH CYCLIC DIADENOSINE TITLE 3 MONOPHOSPHATE (C-DI-AMP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE POTASSIUM TRANSPORT PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 133-217; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS 08BA02176; SOURCE 3 ORGANISM_TAXID: 1229492; SOURCE 4 GENE: C248_1114; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POTASSIUM, TRANSPORTER, KTRA, C-DI-AMP, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KIM,S.J.YOUN,S.O.KIM,J.KO,J.O.LEE,B.S.CHOI REVDAT 5 08-NOV-23 4XTT 1 COMPND SOURCE JRNL REMARK REVDAT 5 2 1 HETNAM REVDAT 4 22-JUL-15 4XTT 1 REMARK REVDAT 3 08-JUL-15 4XTT 1 JRNL REVDAT 2 27-MAY-15 4XTT 1 JRNL REVDAT 1 20-MAY-15 4XTT 0 JRNL AUTH H.KIM,S.J.YOUN,S.O.KIM,J.KO,J.O.LEE,B.S.CHOI JRNL TITL STRUCTURAL STUDIES OF POTASSIUM TRANSPORT PROTEIN KTRA JRNL TITL 2 REGULATOR OF CONDUCTANCE OF K+ (RCK) C DOMAIN IN COMPLEX JRNL TITL 3 WITH CYCLIC DIADENOSINE MONOPHOSPHATE (C-DI-AMP) JRNL REF J.BIOL.CHEM. V. 290 16393 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25957408 JRNL DOI 10.1074/JBC.M115.641340 REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8969 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 895 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 28.3489 - 4.9141 1.00 1446 163 0.2552 0.2769 REMARK 3 2 4.9141 - 3.9037 1.00 1352 146 0.2115 0.2608 REMARK 3 3 3.9037 - 3.4112 1.00 1328 151 0.1996 0.2405 REMARK 3 4 3.4112 - 3.0997 1.00 1326 144 0.2239 0.3144 REMARK 3 5 3.0997 - 2.8778 1.00 1319 143 0.2464 0.2664 REMARK 3 6 2.8778 - 2.7082 1.00 1303 148 0.2488 0.3214 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.78 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 : 0.005 1394 REMARK 3 ANGLE : 0.997 1890 REMARK 3 CHIRALITY : 0.040 222 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 14.124 526 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 4XTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000206272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9002 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 4J91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PH 6.0, 24.5%(W/V) REMARK 280 PEG6000, 250MM LITHIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 42.78750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.48800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.48800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.18125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.48800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.48800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.39375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.48800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.48800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.18125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.48800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.48800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.39375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.78750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 304 O HOH B 305 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 SER A 188 63.67 36.80 REMARK 500 SER B 188 65.15 38.13 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 2BA A 301 DBREF 4XTT A 133 217 UNP J9USJ9 J9USJ9_STAAU 133 217 DBREF 4XTT B 133 217 UNP J9USJ9 J9USJ9_STAAU 133 217 SEQRES 1 A 85 ALA SER ALA SER VAL LEU ASP TYR LEU GLU LEU ALA ASP SEQRES 2 A 85 GLU HIS SER ILE VAL GLU LEU LYS ALA THR GLU LYS MET SEQRES 3 A 85 ALA GLY GLN SER ILE ILE ASP LEU ASP ILE ARG ALA GLN SEQRES 4 A 85 TYR GLY ILE ASN ILE ILE ALA ILE LYS ARG GLY LYS GLU SEQRES 5 A 85 PHE ILE ILE SER PRO ASN PRO ASN ILE ASN LEU GLU ILE SEQRES 6 A 85 GLY ASP ILE LEU ILE MET ILE GLY HIS ASP ASN ASP LEU SEQRES 7 A 85 ASN ARG PHE GLU LYS ASN ILE SEQRES 1 B 85 ALA SER ALA SER VAL LEU ASP TYR LEU GLU LEU ALA ASP SEQRES 2 B 85 GLU HIS SER ILE VAL GLU LEU LYS ALA THR GLU LYS MET SEQRES 3 B 85 ALA GLY GLN SER ILE ILE ASP LEU ASP ILE ARG ALA GLN SEQRES 4 B 85 TYR GLY ILE ASN ILE ILE ALA ILE LYS ARG GLY LYS GLU SEQRES 5 B 85 PHE ILE ILE SER PRO ASN PRO ASN ILE ASN LEU GLU ILE SEQRES 6 B 85 GLY ASP ILE LEU ILE MET ILE GLY HIS ASP ASN ASP LEU SEQRES 7 B 85 ASN ARG PHE GLU LYS ASN ILE HET 2BA A 301 44 HETNAM 2BA (2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6- HETNAM 2 2BA AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3', HETNAM 3 2BA 2'-J][1,3,7,9,2,8 ]TETRAOXADIPHOSPHACYCLODODECINE-3,5, HETNAM 4 2BA 10,12-TETROL 5,12-DIOXIDE HETSYN 2BA BIS-(3',5')-CYCLIC-DIMERIC-ADENOSINE-MONOPHOSPHATE FORMUL 3 2BA C20 H24 N10 O12 P2 FORMUL 4 HOH *20(H2 O) HELIX 1 AA1 SER A 134 ALA A 144 1 11 HELIX 2 AA2 ASP A 167 GLY A 173 1 7 HELIX 3 AA3 ASP A 207 ASN A 216 1 10 HELIX 4 AA4 SER B 134 ASP B 145 1 12 HELIX 5 AA5 ASP B 167 GLY B 173 1 7 HELIX 6 AA6 HIS B 206 ASN B 216 1 11 SHEET 1 AA1 4 HIS A 147 LYS A 153 0 SHEET 2 AA1 4 ILE A 200 HIS A 206 -1 O MET A 203 N VAL A 150 SHEET 3 AA1 4 ASN A 175 ARG A 181 -1 N LYS A 180 O ILE A 200 SHEET 4 AA1 4 GLU A 184 ILE A 187 -1 O ILE A 186 N ILE A 179 SHEET 1 AA2 4 ILE B 149 LYS B 153 0 SHEET 2 AA2 4 ILE B 200 ILE B 204 -1 O LEU B 201 N LEU B 152 SHEET 3 AA2 4 ASN B 175 ARG B 181 -1 N ALA B 178 O ILE B 202 SHEET 4 AA2 4 GLU B 184 ILE B 187 -1 O ILE B 186 N ILE B 179 SITE 1 AC1 19 ILE A 163 ILE A 164 ASP A 167 ILE A 168 SITE 2 AC1 19 ARG A 169 ALA A 170 ILE A 174 ILE A 176 SITE 3 AC1 19 PRO A 191 HOH A 404 ILE B 163 ILE B 164 SITE 4 AC1 19 ASP B 167 ARG B 169 ALA B 170 ILE B 174 SITE 5 AC1 19 ASN B 175 ILE B 176 PRO B 191 CRYST1 84.976 84.976 85.575 90.00 90.00 90.00 P 43 21 2 16 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 0.011768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011686 0.00000