HEADER TRANSFERASE 08-JAN-21 7DUD TITLE CRYSTAL STRUCTURE OF ERWALK COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN KINASE WALK; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.13.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: WALK, SAMEA103891408_00013, SAMEA103891434_00037; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS WALK, YYCG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.HUANG REVDAT 2 29-NOV-23 7DUD 1 REMARK REVDAT 1 19-JAN-22 7DUD 0 JRNL AUTH W.HUANG JRNL TITL CRYSTAL STRUCTURE OF ERWALK JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1988 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 21.0400 - 4.6900 1.00 1905 143 0.2208 0.2264 REMARK 3 2 4.6900 - 3.7300 1.00 1928 138 0.2005 0.2421 REMARK 3 3 3.7200 - 3.2600 1.00 1919 150 0.2146 0.2380 REMARK 3 4 3.2600 - 2.9600 1.00 1932 146 0.2305 0.2297 REMARK 3 5 2.9600 - 2.7500 1.00 1895 141 0.2413 0.2842 REMARK 3 6 2.7500 - 2.5900 1.00 1937 138 0.2448 0.2366 REMARK 3 7 2.5900 - 2.4600 1.00 1928 138 0.2459 0.2721 REMARK 3 8 2.4600 - 2.3500 1.00 1917 148 0.2266 0.2572 REMARK 3 9 2.3500 - 2.2600 1.00 1923 134 0.2289 0.2727 REMARK 3 10 2.2600 - 2.1800 1.00 1921 144 0.2320 0.2647 REMARK 3 11 2.1800 - 2.1200 1.00 1941 138 0.2220 0.2408 REMARK 3 12 2.1200 - 2.0600 1.00 1918 146 0.2252 0.2934 REMARK 3 13 2.0500 - 2.0000 1.00 1889 142 0.2482 0.2836 REMARK 3 14 2.0000 - 1.9500 1.00 1916 142 0.2602 0.2838 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.08 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 : 0.011 2392 REMARK 3 ANGLE : 1.208 3218 REMARK 3 CHIRALITY : 0.074 364 REMARK 3 PLANARITY : 0.007 420 REMARK 3 DIHEDRAL : 21.678 926 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 7DUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020180. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9891 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 4YWZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 AMMONIUM CITRATE, 18 % W/V PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 53.38867 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 26.69433 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 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 MET A 4 REMARK 465 ASN A 5 REMARK 465 MET B 4 REMARK 465 ASN B 5 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 287 O HOH B 292 2.06 REMARK 500 OD1 ASP A 35 O HOH A 201 2.08 REMARK 500 O HOH A 205 O HOH A 209 2.09 REMARK 500 O HOH A 216 O HOH A 290 2.10 REMARK 500 O HOH A 229 O HOH B 246 2.17 REMARK 500 O HOH A 266 O HOH A 275 2.17 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 ASN B 41 -5.69 -141.63 REMARK 500 ASN B 84 -3.17 76.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 307 DISTANCE = 6.65 ANGSTROMS DBREF1 7DUD A 5 152 UNP A0A6K0X802_STAAU DBREF2 7DUD A A0A6K0X802 35 182 DBREF1 7DUD B 5 152 UNP A0A6K0X802_STAAU DBREF2 7DUD B A0A6K0X802 35 182 SEQADV 7DUD MET A 4 UNP A0A6K0X80 INITIATING METHIONINE SEQADV 7DUD CYS A 56 UNP A0A6K0X80 ARG 86 CONFLICT SEQADV 7DUD MET B 4 UNP A0A6K0X80 INITIATING METHIONINE SEQADV 7DUD CYS B 56 UNP A0A6K0X80 ARG 86 CONFLICT SEQRES 1 A 149 MET ASN ASN LEU GLU LYS GLU LEU LEU ASP ASN PHE LYS SEQRES 2 A 149 LYS ASN ILE THR GLN TYR ALA LYS GLN LEU GLU ILE SER SEQRES 3 A 149 ILE GLU LYS VAL TYR ASP GLU LYS GLY SER VAL ASN ALA SEQRES 4 A 149 GLN LYS ASP ILE GLN ASN LEU LEU SER GLU TYR ALA ASN SEQRES 5 A 149 CYS GLN GLU ILE GLY GLU ILE ARG PHE ILE ASP LYS ASP SEQRES 6 A 149 GLN ILE ILE ILE ALA THR THR LYS GLN SER ASN ARG SER SEQRES 7 A 149 LEU ILE ASN GLN LYS ALA ASN ASP SER SER VAL GLN LYS SEQRES 8 A 149 ALA LEU SER LEU GLY GLN SER ASN ASP HIS LEU ILE LEU SEQRES 9 A 149 LYS ASP TYR GLY GLY GLY LYS ASP ARG VAL TRP VAL TYR SEQRES 10 A 149 ASN ILE PRO VAL LYS VAL ASP LYS LYS VAL ILE GLY ASN SEQRES 11 A 149 ILE TYR ILE GLU SER LYS ILE ASN ASP VAL TYR ASN GLN SEQRES 12 A 149 LEU ASN ASN ILE ASN GLN SEQRES 1 B 149 MET ASN ASN LEU GLU LYS GLU LEU LEU ASP ASN PHE LYS SEQRES 2 B 149 LYS ASN ILE THR GLN TYR ALA LYS GLN LEU GLU ILE SER SEQRES 3 B 149 ILE GLU LYS VAL TYR ASP GLU LYS GLY SER VAL ASN ALA SEQRES 4 B 149 GLN LYS ASP ILE GLN ASN LEU LEU SER GLU TYR ALA ASN SEQRES 5 B 149 CYS GLN GLU ILE GLY GLU ILE ARG PHE ILE ASP LYS ASP SEQRES 6 B 149 GLN ILE ILE ILE ALA THR THR LYS GLN SER ASN ARG SER SEQRES 7 B 149 LEU ILE ASN GLN LYS ALA ASN ASP SER SER VAL GLN LYS SEQRES 8 B 149 ALA LEU SER LEU GLY GLN SER ASN ASP HIS LEU ILE LEU SEQRES 9 B 149 LYS ASP TYR GLY GLY GLY LYS ASP ARG VAL TRP VAL TYR SEQRES 10 B 149 ASN ILE PRO VAL LYS VAL ASP LYS LYS VAL ILE GLY ASN SEQRES 11 B 149 ILE TYR ILE GLU SER LYS ILE ASN ASP VAL TYR ASN GLN SEQRES 12 B 149 LEU ASN ASN ILE ASN GLN FORMUL 3 HOH *201(H2 O) HELIX 1 AA1 ASN A 6 GLN A 43 1 38 HELIX 2 AA2 ASP A 45 ALA A 54 1 10 HELIX 3 AA3 LYS A 76 ILE A 83 5 8 HELIX 4 AA4 ASP A 89 GLY A 99 1 11 HELIX 5 AA5 ILE A 140 ILE A 150 1 11 HELIX 6 AA6 LEU B 7 GLY B 38 1 32 HELIX 7 AA7 ASP B 45 ALA B 54 1 10 HELIX 8 AA8 LYS B 76 ILE B 83 5 8 HELIX 9 AA9 ASP B 89 GLY B 99 1 11 HELIX 10 AB1 ILE B 140 ILE B 150 1 11 SHEET 1 AA1 5 ILE A 71 THR A 74 0 SHEET 2 AA1 5 ILE A 59 ASP A 66 -1 N PHE A 64 O ILE A 72 SHEET 3 AA1 5 LYS A 129 SER A 138 -1 O GLU A 137 N GLY A 60 SHEET 4 AA1 5 LYS A 114 VAL A 126 -1 N ILE A 122 O ILE A 134 SHEET 5 AA1 5 ASN A 102 ASP A 109 -1 N HIS A 104 O VAL A 119 SHEET 1 AA2 5 ILE B 71 THR B 74 0 SHEET 2 AA2 5 ILE B 59 ASP B 66 -1 N PHE B 64 O ILE B 72 SHEET 3 AA2 5 LYS B 129 SER B 138 -1 O GLU B 137 N GLY B 60 SHEET 4 AA2 5 LYS B 114 VAL B 126 -1 N VAL B 124 O ILE B 131 SHEET 5 AA2 5 ASN B 102 ASP B 109 -1 N HIS B 104 O VAL B 119 CRYST1 66.630 66.630 80.083 90.00 90.00 120.00 P 32 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 0.015008 0.008665 0.000000 0.00000 SCALE2 0.000000 0.017330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012487 0.00000