HEADER HYDROLASE 05-MAY-13 4KK4 TITLE YWLE ARGININE PHOSPHATASE - C7S MUTANT WITH PHOSPHORYLATED ACTIVE SITE TITLE 2 SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE YWLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LMPTP; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YWLE, BSU36930, IPC-31D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN MODIFICATION, ARGININE PHOSPHORYLATION, ARGININE KEYWDS 2 DEPHOSPHORYLATION, PHOSPHATASE REACTION INTERMEDIATE, LMW PTP, KEYWDS 3 PHOSPHORYLATION AT SER6, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.FUHRMANN,T.CLAUSEN REVDAT 2 17-JUL-13 4KK4 1 JRNL REVDAT 1 03-JUL-13 4KK4 0 JRNL AUTH J.FUHRMANN,B.MIERZWA,D.B.TRENTINI,S.SPIESS,A.LEHNER, JRNL AUTH 2 E.CHARPENTIER,T.CLAUSEN JRNL TITL STRUCTURAL BASIS FOR RECOGNIZING PHOSPHOARGININE AND JRNL TITL 2 EVOLVING RESIDUE-SPECIFIC PROTEIN PHOSPHATASES IN JRNL TITL 3 GRAM-POSITIVE BACTERIA. JRNL REF CELL REP V. 3 1832 2013 JRNL REFN ESSN 2211-1247 JRNL PMID 23770242 JRNL DOI 10.1016/J.CELREP.2013.05.023 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 12465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 571 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 18.4148 - 3.5922 0.88 2587 123 0.1629 0.1810 REMARK 3 2 3.5922 - 2.8547 0.91 2677 139 0.1662 0.2196 REMARK 3 3 2.8547 - 2.4948 0.94 2729 137 0.1671 0.2028 REMARK 3 4 2.4948 - 2.2672 0.93 2749 141 0.1640 0.2290 REMARK 3 5 2.2672 - 2.1049 0.94 2764 160 0.1715 0.2323 REMARK 3 6 2.1049 - 1.9810 0.94 2752 144 0.1889 0.2815 REMARK 3 7 1.9810 - 1.8819 0.93 2699 130 0.2181 0.2571 REMARK 3 8 1.8819 - 1.8000 0.93 2764 160 0.2416 0.2635 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.77 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 : 0.007 1227 REMARK 3 ANGLE : 1.031 1653 REMARK 3 CHIRALITY : 0.071 186 REMARK 3 PLANARITY : 0.004 214 REMARK 3 DIHEDRAL : 14.545 465 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): 12.7906 -18.2339 12.3470 REMARK 3 T TENSOR REMARK 3 T11: 0.1606 T22: 0.1686 REMARK 3 T33: 0.1886 T12: -0.0101 REMARK 3 T13: 0.0092 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.6484 L22: 1.7475 REMARK 3 L33: 2.7752 L12: -0.2945 REMARK 3 L13: 0.6852 L23: -0.2731 REMARK 3 S TENSOR REMARK 3 S11: 0.0328 S12: -0.0202 S13: -0.0556 REMARK 3 S21: 0.0603 S22: 0.0218 S23: 0.0773 REMARK 3 S31: 0.0564 S32: -0.1196 S33: 0.0014 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 4KK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-13. REMARK 100 THE RCSB ID CODE IS RCSB079438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12470 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.919 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : 0.39500 REMARK 200 FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG400, 50 MM TRIS-HCL, PH 6.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 42.92000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.92000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.67000 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 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: 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 SEP A 7 -155.09 -127.69 REMARK 500 CYS A 12 -84.59 -130.10 REMARK 500 ASN A 44 -7.02 77.89 REMARK 500 LEU A 151 2.78 -62.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KK3 RELATED DB: PDB DBREF 4KK4 A 1 150 UNP P39155 YWLE_BACSU 1 150 SEQADV 4KK4 SEP A 7 UNP P39155 CYS 7 ENGINEERED MUTATION SEQADV 4KK4 LEU A 151 UNP P39155 EXPRESSION TAG SEQADV 4KK4 GLU A 152 UNP P39155 EXPRESSION TAG SEQRES 1 A 152 MET ASP ILE ILE PHE VAL SEP THR GLY ASN THR CYS ARG SEQRES 2 A 152 SER PRO MET ALA GLU ALA LEU PHE LYS SER ILE ALA GLU SEQRES 3 A 152 ARG GLU GLY LEU ASN VAL ASN VAL ARG SER ALA GLY VAL SEQRES 4 A 152 PHE ALA SER PRO ASN GLY LYS ALA THR PRO HIS ALA VAL SEQRES 5 A 152 GLU ALA LEU PHE GLU LYS HIS ILE ALA LEU ASN HIS VAL SEQRES 6 A 152 SER SER PRO LEU THR GLU GLU LEU MET GLU SER ALA ASP SEQRES 7 A 152 LEU VAL LEU ALA MET THR HIS GLN HIS LYS GLN ILE ILE SEQRES 8 A 152 ALA SER GLN PHE GLY ARG TYR ARG ASP LYS VAL PHE THR SEQRES 9 A 152 LEU LYS GLU TYR VAL THR GLY SER HIS GLY ASP VAL LEU SEQRES 10 A 152 ASP PRO PHE GLY GLY SER ILE ASP ILE TYR LYS GLN THR SEQRES 11 A 152 ARG ASP GLU LEU GLU GLU LEU LEU ARG GLN LEU ALA LYS SEQRES 12 A 152 GLN LEU LYS LYS ASP ARG ARG LEU GLU MODRES 4KK4 SEP A 7 SER PHOSPHOSERINE HET SEP A 7 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 HOH *59(H2 O) HELIX 1 1 CYS A 12 GLY A 29 1 18 HELIX 2 2 THR A 48 GLU A 57 1 10 HELIX 3 3 THR A 70 ALA A 77 1 8 HELIX 4 4 THR A 84 PHE A 95 1 12 HELIX 5 5 GLY A 96 ASP A 100 5 5 HELIX 6 6 LEU A 105 GLY A 111 1 7 HELIX 7 7 SER A 123 LYS A 146 1 24 HELIX 8 8 LYS A 147 GLU A 152 5 6 SHEET 1 A 4 ASN A 33 GLY A 38 0 SHEET 2 A 4 ASP A 2 SEP A 7 1 N ILE A 3 O ASN A 33 SHEET 3 A 4 LEU A 79 ALA A 82 1 O LEU A 81 N ILE A 4 SHEET 4 A 4 VAL A 102 THR A 104 1 O PHE A 103 N ALA A 82 LINK C VAL A 6 N SEP A 7 1555 1555 1.34 LINK C SEP A 7 N THR A 8 1555 1555 1.33 CRYST1 85.840 39.340 40.670 90.00 89.70 90.00 C 1 2 1 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 0.011650 0.000000 -0.000061 0.00000 SCALE2 0.000000 0.025419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024588 0.00000