HEADER HYDROLASE 17-JAN-18 5Z59 TITLE CRYSTAL STRUCTURE OF TK-PTP IN THE INACTIVE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-TYROSINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 SOURCE 3 / JCM 12380 / KOD1); SOURCE 4 ORGANISM_COMMON: PYROCOCCUS KODAKARAENSIS (STRAIN KOD1); SOURCE 5 ORGANISM_TAXID: 69014; SOURCE 6 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 7 GENE: TK-PTP, TK0241; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TYROSINE PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.KU,H.Y.YUN,S.J.KIM REVDAT 2 22-NOV-23 5Z59 1 REMARK REVDAT 1 27-JUN-18 5Z59 0 JRNL AUTH H.Y.YUN,J.LEE,H.KIM,H.RYU,H.C.SHIN,B.H.OH,B.KU,S.J.KIM JRNL TITL STRUCTURAL STUDY REVEALS THE TEMPERATURE-DEPENDENT JRNL TITL 2 CONFORMATIONAL FLEXIBILITY OF TK-PTP, A PROTEIN TYROSINE JRNL TITL 3 PHOSPHATASE FROM THERMOCOCCUS KODAKARAENSIS KOD1 JRNL REF PLOS ONE V. 13 97635 2018 JRNL REFN ESSN 1932-6203 JRNL PMID 29791483 JRNL DOI 10.1371/JOURNAL.PONE.0197635 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.560 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 13084 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1308 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 31.0367 - 3.5410 0.97 1419 158 0.1590 0.1705 REMARK 3 2 3.5410 - 2.8112 0.99 1353 150 0.1736 0.2360 REMARK 3 3 2.8112 - 2.4560 0.99 1323 148 0.2020 0.2323 REMARK 3 4 2.4560 - 2.2315 0.99 1332 148 0.1952 0.2716 REMARK 3 5 2.2315 - 2.0716 0.98 1308 145 0.1852 0.2234 REMARK 3 6 2.0716 - 1.9495 0.97 1272 140 0.1990 0.2939 REMARK 3 7 1.9495 - 1.8519 0.97 1283 143 0.2199 0.2834 REMARK 3 8 1.8519 - 1.7713 0.95 1266 140 0.2405 0.2770 REMARK 3 9 1.7713 - 1.7031 0.93 1220 136 0.2559 0.3240 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.000 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 : 0.007 1206 REMARK 3 ANGLE : 0.905 1628 REMARK 3 CHIRALITY : 0.056 176 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 18.005 737 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 5Z59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 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: 2I6I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE (PH 5.4), 8%(W/V) REMARK 280 POLYETHYLENE GLYCOL 10000, 14%(V/V) DIOXANE, VAPOR DIFFUSION, REMARK 280 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 14.73650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.26900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.31900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.26900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.73650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.31900 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 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 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 ALA A 27 O HOH A 201 2.04 REMARK 500 O HOH A 273 O HOH A 295 2.09 REMARK 500 O HOH A 297 O HOH A 301 2.10 REMARK 500 O HOH A 287 O HOH A 299 2.15 REMARK 500 O HOH A 201 O HOH A 233 2.16 REMARK 500 O HOH A 202 O HOH A 299 2.16 REMARK 500 O HOH A 201 O HOH A 223 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 ASP A 9 -156.81 -147.31 REMARK 500 LYS A 51 -9.43 -58.96 REMARK 500 CYS A 93 -131.79 -131.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z59 A 1 147 UNP Q8X270 Q8X270_THEKO 1 147 SEQRES 1 A 147 MET TRP PRO SER ALA LYS PHE ILE ASP GLY ARG VAL ALA SEQRES 2 A 147 PHE SER ARG MET PRO ALA GLU ARG GLU LEU ASP GLU VAL SEQRES 3 A 147 ALA ARG ASP PHE ASP ALA VAL VAL VAL LEU VAL GLU ASP SEQRES 4 A 147 TYR GLU LEU PRO TYR SER LEU ASP GLU TRP GLU LYS ARG SEQRES 5 A 147 GLY VAL GLU VAL LEU HIS GLY PRO ILE PRO ASP PHE THR SEQRES 6 A 147 ALA PRO SER VAL GLU GLN LEU LEU GLU ILE LEU ARG TRP SEQRES 7 A 147 ILE GLU GLU ARG VAL ARG GLU GLY LYS LYS VAL LEU ILE SEQRES 8 A 147 HIS CYS MET GLY GLY LEU GLY ARG SER GLY THR VAL GLY SEQRES 9 A 147 VAL ALA TRP LEU MET TYR SER ARG GLY LEU SER LEU ARG SEQRES 10 A 147 GLU ALA LEU MET GLU VAL ARG ARG LYS ARG PRO GLY ALA SEQRES 11 A 147 VAL GLU THR GLN GLU GLN MET GLU VAL LEU LYS GLU LEU SEQRES 12 A 147 GLU GLU ARG ILE FORMUL 2 HOH *106(H2 O) HELIX 1 AA1 ALA A 19 ARG A 21 5 3 HELIX 2 AA2 GLU A 22 ARG A 28 1 7 HELIX 3 AA3 GLU A 38 LEU A 42 5 5 HELIX 4 AA4 LEU A 46 LYS A 51 1 6 HELIX 5 AA5 SER A 68 GLU A 85 1 18 HELIX 6 AA6 LEU A 97 GLY A 113 1 17 HELIX 7 AA7 SER A 115 ARG A 127 1 13 HELIX 8 AA8 THR A 133 ILE A 147 1 15 SHEET 1 AA1 5 LYS A 6 PHE A 7 0 SHEET 2 AA1 5 VAL A 12 SER A 15 -1 O PHE A 14 N LYS A 6 SHEET 3 AA1 5 VAL A 89 HIS A 92 1 O ILE A 91 N ALA A 13 SHEET 4 AA1 5 ALA A 32 VAL A 35 1 N VAL A 34 O LEU A 90 SHEET 5 AA1 5 GLU A 55 HIS A 58 1 O LEU A 57 N VAL A 35 CRYST1 29.473 50.638 78.538 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 0.033929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012733 0.00000