HEADER TRANSFERASE 26-JAN-17 5X1R TITLE PPKA-294 APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PPKA-294; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA SP. FS14; SOURCE 3 ORGANISM_TAXID: 1327989; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.P.LI,T.T.RAN,D.Q.XU,W.W.WANG REVDAT 3 20-MAR-24 5X1R 1 REMARK REVDAT 2 21-AUG-19 5X1R 1 JRNL REVDAT 1 31-JAN-18 5X1R 0 JRNL AUTH P.P.LI,D.Q.XU,T.Q.MA,D.Y.WANG,W.D.LI,J.H.HE,T.T.RAN,W.W.WANG JRNL TITL CRYSTAL STRUCTURES OF THE KINASE DOMAIN OF PPKA, A KEY JRNL TITL 2 REGULATORY COMPONENT OF T6SS, REVEAL A GENERAL INHIBITORY JRNL TITL 3 MECHANISM. JRNL REF BIOCHEM.J. V. 475 2209 2018 JRNL REFN ESSN 1470-8728 JRNL PMID 29858276 JRNL DOI 10.1042/BCJ20180077 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2247: ???) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 - 3.8556 1.00 2973 151 0.1620 0.1940 REMARK 3 2 3.8556 - 3.0605 1.00 2828 148 0.1825 0.2153 REMARK 3 3 3.0605 - 2.6737 1.00 2794 145 0.1956 0.2271 REMARK 3 4 2.6737 - 2.4292 1.00 2780 152 0.1978 0.1963 REMARK 3 5 2.4292 - 2.2551 1.00 2780 128 0.1880 0.2143 REMARK 3 6 2.2551 - 2.1222 1.00 2774 131 0.1871 0.2498 REMARK 3 7 2.1222 - 2.0159 1.00 2763 134 0.1971 0.2089 REMARK 3 8 2.0159 - 1.9281 1.00 2720 153 0.1932 0.2568 REMARK 3 9 1.9281 - 1.8539 1.00 2784 116 0.2007 0.2294 REMARK 3 10 1.8539 - 1.7899 1.00 2720 142 0.1908 0.2260 REMARK 3 11 1.7899 - 1.7339 1.00 2694 164 0.1880 0.2241 REMARK 3 12 1.7339 - 1.6844 1.00 2757 149 0.2014 0.2057 REMARK 3 13 1.6844 - 1.6400 1.00 2700 150 0.2055 0.2490 REMARK 3 14 1.6400 - 1.6000 0.94 2553 136 0.2405 0.2937 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.010 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) : 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 : 0.008 2318 REMARK 3 ANGLE : 1.065 3145 REMARK 3 CHIRALITY : 0.055 341 REMARK 3 PLANARITY : 0.006 416 REMARK 3 DIHEDRAL : 15.598 1395 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 5X1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-15 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 : 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) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40724 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 44.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM CHLORIDE, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.15000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.15000 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 GLY A 5 REMARK 465 ILE A 6 REMARK 465 THR A 7 REMARK 465 LYS A 8 REMARK 465 PRO A 9 REMARK 465 ASN A 10 REMARK 465 GLU A 214 REMARK 465 ASN A 215 REMARK 465 SER A 216 REMARK 465 ASP A 217 REMARK 465 GLY A 218 REMARK 465 HIS A 297 REMARK 465 HIS A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 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 NH2 ARG A 106 O HOH A 401 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 106 CG - CD - NE ANGL. DEV. = -26.3 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES 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 A 21 -114.72 49.98 REMARK 500 MET A 55 78.74 -159.93 REMARK 500 THR A 113 -157.57 -147.88 REMARK 500 ASP A 165 25.73 -140.15 REMARK 500 GLN A 177 -3.71 78.59 REMARK 500 ASP A 183 138.52 -171.63 REMARK 500 VAL A 201 -70.00 -92.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X1Q RELATED DB: PDB REMARK 900 RELATED ID: 5X1S RELATED DB: PDB REMARK 900 RELATED ID: 5X1T RELATED DB: PDB DBREF 5X1R A 1 302 PDB 5X1R 5X1R 1 302 SEQRES 1 A 302 MET SER GLY THR GLY ILE THR LYS PRO ASN SER ASN SER SEQRES 2 A 302 LEU PRO SER GLY TYR ARG PHE ASN GLU PHE GLU ILE GLN SEQRES 3 A 302 GLU ALA ILE GLY GLU GLY GLY PHE GLY ILE VAL TYR ARG SEQRES 4 A 302 ALA TYR ASP HIS GLN LEU GLU ARG THR ILE ALA ILE LYS SEQRES 5 A 302 GLU TYR MET PRO THR SER LEU ALA LYS ARG ASN ASP ASP SEQRES 6 A 302 LEU SER ILE GLY LEU ARG GLY GLU ARG PHE GLY LYS THR SEQRES 7 A 302 PHE GLN ALA GLY LEU ASN SER PHE ILE GLN GLU ALA ARG SEQRES 8 A 302 LEU LEU ALA ARG PHE SER HIS PRO GLY LEU LEU HIS VAL SEQRES 9 A 302 LEU ARG PHE TRP GLU GLU ASN GLY THR ALA TYR MET GLY SEQRES 10 A 302 THR GLN PHE TYR SER GLY THR THR LEU LYS ASN LEU GLN SEQRES 11 A 302 ALA GLN GLN PRO GLU LYS ILE ASP GLU ALA TRP ILE ARG SEQRES 12 A 302 ARG LEU LEU PRO PRO LEU PHE SER ALA ILE ASN THR ILE SEQRES 13 A 302 HIS GLN GLU GLY TYR LEU HIS ARG ASP ILE SER LEU ASP SEQRES 14 A 302 ASN ILE GLN ILE GLN GLU SER GLN LEU PRO VAL LEU LEU SEQRES 15 A 302 ASP PHE GLY SER ALA ARG LYS GLU ILE GLY ASN LEU SER SEQRES 16 A 302 ASP GLU THR GLU ILE VAL LEU LYS PRO GLY PHE ALA PRO SEQRES 17 A 302 ILE GLU GLN TYR THR GLU ASN SER ASP GLY GLU GLN GLY SEQRES 18 A 302 PRO TRP THR ASP ILE TYR ALA LEU GLY ALA VAL LEU HIS SEQRES 19 A 302 THR LEU ILE VAL GLY SER PRO PRO PRO VAL SER VAL VAL SEQRES 20 A 302 ARG SER ILE GLU ASP SER TYR GLN PRO LEU THR GLU ARG SEQRES 21 A 302 ARG PRO ALA GLY TYR SER PRO GLU LEU LEU ARG THR VAL SEQRES 22 A 302 ASP ARG ALA LEU ALA LEU LYS PRO GLU ASP ARG PRO GLN SEQRES 23 A 302 THR ILE ASP GLU MET ALA GLU LEU LEU GLU HIS HIS HIS SEQRES 24 A 302 HIS HIS HIS FORMUL 2 HOH *212(H2 O) HELIX 1 AA1 GLY A 72 ARG A 74 5 3 HELIX 2 AA2 PHE A 75 ALA A 94 1 20 HELIX 3 AA3 LEU A 126 GLN A 133 1 8 HELIX 4 AA4 PRO A 134 ILE A 137 5 4 HELIX 5 AA5 ASP A 138 GLU A 159 1 22 HELIX 6 AA6 SER A 167 ASP A 169 5 3 HELIX 7 AA7 GLY A 185 ASP A 196 1 12 HELIX 8 AA8 GLU A 197 VAL A 201 5 5 HELIX 9 AA9 PRO A 208 THR A 213 5 6 HELIX 10 AB1 GLY A 221 GLY A 239 1 19 HELIX 11 AB2 VAL A 244 GLU A 251 1 8 HELIX 12 AB3 PRO A 256 ARG A 261 1 6 HELIX 13 AB4 SER A 266 LEU A 277 1 12 HELIX 14 AB5 LYS A 280 ARG A 284 5 5 HELIX 15 AB6 THR A 287 LEU A 295 1 9 SHEET 1 AA1 6 ARG A 19 PHE A 20 0 SHEET 2 AA1 6 PHE A 23 GLU A 31 -1 O PHE A 23 N PHE A 20 SHEET 3 AA1 6 GLY A 35 ASP A 42 -1 O VAL A 37 N GLY A 30 SHEET 4 AA1 6 ARG A 47 TYR A 54 -1 O ARG A 47 N ASP A 42 SHEET 5 AA1 6 THR A 113 GLN A 119 -1 O THR A 118 N ALA A 50 SHEET 6 AA1 6 VAL A 104 GLU A 110 -1 N LEU A 105 O GLY A 117 SHEET 1 AA2 2 ALA A 60 ARG A 62 0 SHEET 2 AA2 2 ILE A 68 LEU A 70 -1 O GLY A 69 N LYS A 61 SHEET 1 AA3 3 THR A 124 THR A 125 0 SHEET 2 AA3 3 ILE A 171 ILE A 173 -1 O ILE A 173 N THR A 124 SHEET 3 AA3 3 PRO A 179 LEU A 181 -1 O VAL A 180 N GLN A 172 CRYST1 59.100 65.500 78.300 90.00 90.00 90.00 P 2 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 0.016920 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012771 0.00000