HEADER IMMUNE SYSTEM 16-MAR-15 4YS2 TITLE RCK DOMAIN WITH CDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NA+/H+ ANTIPORTER-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RCK C-TERMINAL DOMAIN (UNP RESIDUES 531-614); COMPND 5 SYNONYM: SODIUM:PROTON ANTIPORTER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTRH1T KEYWDS RCK DOMAIN, CDA, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.H.CHIN,S.H.CHOU REVDAT 2 05-FEB-20 4YS2 1 REMARK REVDAT 1 27-APR-16 4YS2 0 JRNL AUTH K.H.CHIN,S.H.CHOU JRNL TITL RCK DOMAIN WITH CDA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 9460 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 946 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 10.0000 - 3.7562 0.99 1333 151 0.2524 0.2813 REMARK 3 2 3.7562 - 2.9853 0.99 1268 140 0.2403 0.2911 REMARK 3 3 2.9853 - 2.6090 0.98 1229 138 0.2674 0.2859 REMARK 3 4 2.6090 - 2.3710 0.97 1218 133 0.2587 0.2991 REMARK 3 5 2.3710 - 2.2013 0.96 1184 133 0.2402 0.2884 REMARK 3 6 2.2013 - 2.0717 0.93 1158 125 0.2405 0.2647 REMARK 3 7 2.0717 - 1.9681 0.91 1124 126 0.2198 0.2566 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 47.77 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.240 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) : -5.55950 REMARK 3 B22 (A**2) : 5.65330 REMARK 3 B33 (A**2) : -0.09380 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 1238 REMARK 3 ANGLE : 1.176 1670 REMARK 3 CHIRALITY : 0.081 178 REMARK 3 PLANARITY : 0.005 218 REMARK 3 DIHEDRAL : 16.843 470 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.9767 -0.2102 -6.6127 REMARK 3 T TENSOR REMARK 3 T11: 0.2213 T22: 0.1853 REMARK 3 T33: 0.1886 T12: -0.0186 REMARK 3 T13: -0.0020 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.1389 L22: 1.4125 REMARK 3 L33: 1.2486 L12: -0.4913 REMARK 3 L13: -0.7370 L23: -0.0692 REMARK 3 S TENSOR REMARK 3 S11: -0.0937 S12: 0.0208 S13: -0.1091 REMARK 3 S21: -0.0145 S22: 0.0246 S23: 0.0926 REMARK 3 S31: 0.0997 S32: 0.0061 S33: 0.0741 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 4YS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12747 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5 AND 1.1M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, 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 20.59750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.89500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.92150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.89500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.59750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.92150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 132 REMARK 465 ASN A 133 REMARK 465 MSE A 134 REMARK 465 LEU A 135 REMARK 465 ASN A 136 REMARK 465 LEU A 137 REMARK 465 LEU A 138 REMARK 465 SER A 139 REMARK 465 ASN A 140 REMARK 465 VAL A 141 REMARK 465 GLU A 142 REMARK 465 PHE A 215 REMARK 465 PRO B 132 REMARK 465 ASN B 133 REMARK 465 MSE B 134 REMARK 465 LEU B 135 REMARK 465 ASN B 136 REMARK 465 LEU B 137 REMARK 465 LEU B 138 REMARK 465 SER B 139 REMARK 465 ASN B 140 REMARK 465 VAL B 141 REMARK 465 GLU B 142 REMARK 465 PHE B 215 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 302 O HOH B 305 2.03 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 B 301 O HOH B 309 4455 2.16 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YP1 RELATED DB: PDB DBREF 4YS2 A 132 215 UNP W8TQN9 W8TQN9_STAAU 531 614 DBREF 4YS2 B 132 215 UNP W8TQN9 W8TQN9_STAAU 531 614 SEQRES 1 A 84 PRO ASN MSE LEU ASN LEU LEU SER ASN VAL GLU THR SER SEQRES 2 A 84 LEU TYR GLU ILE GLN MSE LEU ASN TYR LYS TYR GLU ASN SEQRES 3 A 84 ILE GLN LEU ARG ASN PHE PRO PHE GLY GLY ASP ILE ILE SEQRES 4 A 84 PHE VAL ARG ILE ILE ARG ASN ASN GLU SER ILE VAL PRO SEQRES 5 A 84 HIS GLY ASP THR GLN LEU ARG TYR GLY ASP ARG LEU ILE SEQRES 6 A 84 VAL THR GLY ALA LYS GLU TYR VAL ASP GLU LEU LYS GLN SEQRES 7 A 84 GLU LEU GLU PHE TYR PHE SEQRES 1 B 84 PRO ASN MSE LEU ASN LEU LEU SER ASN VAL GLU THR SER SEQRES 2 B 84 LEU TYR GLU ILE GLN MSE LEU ASN TYR LYS TYR GLU ASN SEQRES 3 B 84 ILE GLN LEU ARG ASN PHE PRO PHE GLY GLY ASP ILE ILE SEQRES 4 B 84 PHE VAL ARG ILE ILE ARG ASN ASN GLU SER ILE VAL PRO SEQRES 5 B 84 HIS GLY ASP THR GLN LEU ARG TYR GLY ASP ARG LEU ILE SEQRES 6 B 84 VAL THR GLY ALA LYS GLU TYR VAL ASP GLU LEU LYS GLN SEQRES 7 B 84 GLU LEU GLU PHE TYR PHE MODRES 4YS2 MSE A 150 MET MODIFIED RESIDUE MODRES 4YS2 MSE B 150 MET MODIFIED RESIDUE HET MSE A 150 8 HET MSE B 150 8 HET 2BA A 301 44 HETNAM MSE SELENOMETHIONINE 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 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 2BA C20 H24 N10 O12 P2 FORMUL 4 HOH *23(H2 O) HELIX 1 AA1 ASN A 152 GLU A 156 5 5 HELIX 2 AA2 GLN A 159 PHE A 163 5 5 HELIX 3 AA3 ALA A 200 PHE A 213 1 14 HELIX 4 AA4 ASN B 152 GLU B 156 5 5 HELIX 5 AA5 ALA B 200 PHE B 213 1 14 SHEET 1 AA1 4 TYR A 146 GLN A 149 0 SHEET 2 AA1 4 ARG A 194 THR A 198 -1 O LEU A 195 N ILE A 148 SHEET 3 AA1 4 ILE A 170 ARG A 176 -1 N ILE A 175 O ARG A 194 SHEET 4 AA1 4 GLU A 179 ILE A 181 -1 O ILE A 181 N ILE A 174 SHEET 1 AA2 4 TYR B 146 GLN B 149 0 SHEET 2 AA2 4 ARG B 194 GLY B 199 -1 O LEU B 195 N ILE B 148 SHEET 3 AA2 4 ILE B 169 ARG B 176 -1 N ARG B 173 O ILE B 196 SHEET 4 AA2 4 GLU B 179 ILE B 181 -1 O ILE B 181 N ILE B 174 LINK C GLN A 149 N MSE A 150 1555 1555 1.33 LINK C MSE A 150 N LEU A 151 1555 1555 1.33 LINK C GLN B 149 N MSE B 150 1555 1555 1.33 LINK C MSE B 150 N LEU B 151 1555 1555 1.33 SITE 1 AC1 17 LEU A 160 ARG A 161 PHE A 165 ILE A 170 SITE 2 AC1 17 PHE A 171 PRO A 183 HIS A 184 GLY A 185 SITE 3 AC1 17 HOH A 403 HOH A 404 LEU B 160 ARG B 161 SITE 4 AC1 17 ILE B 170 PHE B 171 PRO B 183 HIS B 184 SITE 5 AC1 17 GLY B 185 CRYST1 41.195 45.843 69.790 90.00 90.00 90.00 P 21 21 21 8 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 0.024275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014329 0.00000