HEADER SIGNALING PROTEIN 19-DEC-19 6LKJ TITLE TWO-COMPONENT SYSTEM PROTEIN MEDIATE SIGNAL TRANSDUCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABC TRANSPORTER, SOLUTE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EXTRACELLULAR SOLUTE-BINDING PROTEIN,IRON ABC TRANSPORTER COMPND 5 SUBSTRATE-BINDING PROTEIN,LIPOPROTEIN,PERIPLASMIC-IRON-BINDING COMPND 6 PROTEIN BITC; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: E4U00_07700, EP54_06205, EQ90_12025, HMPREF3211_02751, SOURCE 5 NCTC10654_00249, NCTC10702_00414, RK64_01575; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TWO-COMPONENT SYSTEM, G6P SENSOR, SIGNAL TRANSDUCTION, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.WANG,Y.TAO REVDAT 3 27-MAR-24 6LKJ 1 REMARK REVDAT 2 16-DEC-20 6LKJ 1 JRNL REVDAT 1 02-DEC-20 6LKJ 0 JRNL AUTH M.WANG,Q.GUO,K.ZHU,B.FANG,Y.YANG,M.TENG,X.LI,Y.TAO JRNL TITL INTERFACE SWITCH MEDIATES SIGNAL TRANSMISSION IN A JRNL TITL 2 TWO-COMPONENT SYSTEM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 30433 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33199635 JRNL DOI 10.1073/PNAS.1912080117 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 21110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 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 28.2350 - 3.8303 0.96 2943 139 0.1675 0.1939 REMARK 3 2 3.8303 - 3.0413 1.00 2899 158 0.1837 0.2296 REMARK 3 3 3.0413 - 2.6572 1.00 2904 141 0.2042 0.2318 REMARK 3 4 2.6572 - 2.4144 1.00 2875 146 0.2066 0.2335 REMARK 3 5 2.4144 - 2.2414 1.00 2821 161 0.2138 0.2475 REMARK 3 6 2.2414 - 2.1093 1.00 2851 135 0.2160 0.2321 REMARK 3 7 2.1093 - 2.0040 0.98 2802 135 0.2344 0.3035 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.12 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 : 0.002 2444 REMARK 3 ANGLE : 0.525 3312 REMARK 3 CHIRALITY : 0.045 371 REMARK 3 PLANARITY : 0.003 425 REMARK 3 DIHEDRAL : 5.373 1487 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 6LKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21110 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 7.5-7.9, 21% PEG 3350, REMARK 280 VAPOR DIFFUSION, 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 26.08200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.57850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.08200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.57850 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 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 502 O HOH A 586 2.11 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 586 O HOH A 622 4445 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 PHE A 123 -54.20 -125.40 REMARK 500 SER A 215 -157.02 -132.87 REMARK 500 ASP A 286 30.12 -99.30 REMARK 500 GLN A 293 -119.02 60.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LKJ A 29 322 UNP X5DVD1 X5DVD1_STAAU 29 322 SEQRES 1 A 294 ASN VAL LEU THR VAL TYR SER PRO TYR GLN SER ASN LEU SEQRES 2 A 294 ILE ARG PRO ILE LEU ASN GLU PHE GLU LYS GLN GLU HIS SEQRES 3 A 294 VAL LYS ILE GLU ILE LYS HIS GLY SER THR GLN VAL LEU SEQRES 4 A 294 LEU SER ASN LEU HIS ASN GLU ASP PHE SER GLU ARG GLY SEQRES 5 A 294 ASP VAL PHE MET GLY GLY VAL LEU SER GLU THR ILE ASP SEQRES 6 A 294 HIS PRO GLU ASP PHE VAL PRO TYR GLN ASP THR SER VAL SEQRES 7 A 294 THR GLN GLN LEU GLU ASP TYR ARG SER ASN ASN LYS TYR SEQRES 8 A 294 VAL THR SER PHE LEU LEU MET PRO THR VAL ILE VAL VAL SEQRES 9 A 294 ASN SER ASP LEU GLN GLY ASP ILE LYS ILE ARG GLY TYR SEQRES 10 A 294 GLN ASP LEU LEU GLN PRO ILE LEU LYS GLY LYS ILE ALA SEQRES 11 A 294 TYR SER ASN PRO ASN THR THR THR THR GLY TYR GLN HIS SEQRES 12 A 294 MET ARG ALA ILE TYR SER MET HIS HIS ARG VAL SER ASP SEQRES 13 A 294 VAL HIS GLN PHE GLN ASN HIS ALA MET GLN LEU SER LYS SEQRES 14 A 294 THR SER LYS VAL ILE GLU ASP VAL ALA LYS GLY LYS TYR SEQRES 15 A 294 TYR ALA GLY LEU SER TYR GLU GLN ASP ALA ARG THR TRP SEQRES 16 A 294 LYS ASN LYS GLY TYR PRO VAL SER ILE VAL TYR PRO ILE SEQRES 17 A 294 GLU GLY THR MET LEU ASN VAL ASP GLY ILE ALA LEU VAL SEQRES 18 A 294 LYS ASN ALA HIS PRO HIS PRO LYS ARG LYS LYS LEU VAL SEQRES 19 A 294 GLN TYR LEU THR SER ARG SER VAL GLN GLN ARG LEU VAL SEQRES 20 A 294 ALA GLU PHE ASP ALA LYS SER ILE ARG LYS ASP VAL SER SEQRES 21 A 294 GLU GLN SER ASP GLN SER ILE GLU ASN LEU LYS ASN ILE SEQRES 22 A 294 PRO LEU ILE PRO LYS SER LYS LEU PRO ASP ILE PRO HIS SEQRES 23 A 294 HIS LYS PHE LEU GLU MET ILE GLN HET BGP A 401 16 HETNAM BGP 6-O-PHOSPHONO-BETA-D-GALACTOPYRANOSE HETSYN BGP BETA-GALACTOSE-6-PHOSPHATE; 6-O-PHOSPHONO-BETA-D- HETSYN 2 BGP GALACTOSE; 6-O-PHOSPHONO-D-GALACTOSE; 6-O-PHOSPHONO- HETSYN 3 BGP GALACTOSE FORMUL 2 BGP C6 H13 O9 P FORMUL 3 HOH *128(H2 O) HELIX 1 AA1 GLN A 38 HIS A 54 1 17 HELIX 2 AA2 SER A 63 ASN A 73 1 11 HELIX 3 AA3 VAL A 87 ILE A 92 1 6 HELIX 4 AA4 HIS A 94 GLU A 96 5 3 HELIX 5 AA5 ASP A 103 GLN A 109 5 7 HELIX 6 AA6 LEU A 110 ARG A 114 5 5 HELIX 7 AA7 SER A 134 GLY A 138 1 5 HELIX 8 AA8 TYR A 145 LYS A 154 5 10 HELIX 9 AA9 THR A 165 MET A 178 1 14 HELIX 10 AB1 ARG A 181 ALA A 192 1 12 HELIX 11 AB2 LYS A 197 LYS A 207 1 11 HELIX 12 AB3 GLU A 217 LYS A 226 1 10 HELIX 13 AB4 LYS A 257 THR A 266 1 10 HELIX 14 AB5 SER A 267 ASP A 279 1 13 HELIX 15 AB6 ASN A 297 ILE A 301 5 5 HELIX 16 AB7 PRO A 305 LEU A 309 5 5 HELIX 17 AB8 PRO A 313 ILE A 321 1 9 SHEET 1 AA1 8 LYS A 56 HIS A 61 0 SHEET 2 AA1 8 VAL A 30 SER A 35 1 N LEU A 31 O LYS A 56 SHEET 3 AA1 8 VAL A 82 MET A 84 1 O VAL A 82 N TYR A 34 SHEET 4 AA1 8 LEU A 241 VAL A 249 -1 O ALA A 247 N PHE A 83 SHEET 5 AA1 8 THR A 121 ASN A 133 -1 N PHE A 123 O ASP A 244 SHEET 6 AA1 8 ALA A 212 TYR A 216 -1 O GLY A 213 N VAL A 131 SHEET 7 AA1 8 ILE A 157 SER A 160 1 N ALA A 158 O LEU A 214 SHEET 8 AA1 8 MET A 193 LEU A 195 1 O LEU A 195 N TYR A 159 SHEET 1 AA2 4 PHE A 98 VAL A 99 0 SHEET 2 AA2 4 LEU A 241 VAL A 249 -1 O LEU A 248 N VAL A 99 SHEET 3 AA2 4 THR A 121 ASN A 133 -1 N PHE A 123 O ASP A 244 SHEET 4 AA2 4 LYS A 281 SER A 282 -1 O LYS A 281 N LEU A 125 SHEET 1 AA3 3 VAL A 230 VAL A 233 0 SHEET 2 AA3 3 THR A 121 ASN A 133 -1 N ILE A 130 O VAL A 233 SHEET 3 AA3 3 LYS A 281 SER A 282 -1 O LYS A 281 N LEU A 125 CRYST1 52.164 67.157 87.600 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 0.019170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011416 0.00000