HEADER SIGNALING PROTEIN 01-APR-20 7BTG TITLE CRYSTAL STRUCTURE OF DARP, DROSOPHILA ARGININE PHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GEO10716P1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG9599, DMEL\CG31469, CG31469, DMEL_CG31469; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARGININE PHOSPHATASE, LMWPTP, LMW-PTP, DARP, DROSOPHILA, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.S.LEE,Y.MO,B.KU,S.J.KIM REVDAT 2 29-NOV-23 7BTG 1 REMARK REVDAT 1 13-JAN-21 7BTG 0 JRNL AUTH H.S.LEE,Y.MO,H.C.SHIN,S.J.KIM,B.KU JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE TWO JRNL TITL 2 DROSOPHILA LOW MOLECULAR WEIGHT-PROTEIN TYROSINE JRNL TITL 3 PHOSPHATASES DARP AND PRIMO-1. JRNL REF MOL.CELLS V. 43 1035 2020 JRNL REFN ISSN 1016-8478 JRNL PMID 33372666 JRNL DOI 10.14348/MOLCELLS.2020.0192 REMARK 2 REMARK 2 RESOLUTION. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 9483 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 949 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 30.8720 - 4.1830 0.99 1321 148 0.1746 0.2123 REMARK 3 2 4.1830 - 3.3214 0.99 1249 138 0.1832 0.2285 REMARK 3 3 3.3214 - 2.9019 0.99 1231 137 0.2279 0.2951 REMARK 3 4 2.9019 - 2.6367 0.98 1196 133 0.2386 0.2725 REMARK 3 5 2.6367 - 2.4478 0.99 1214 135 0.2413 0.3306 REMARK 3 6 2.4478 - 2.3036 0.97 1181 132 0.2366 0.2827 REMARK 3 7 2.3036 - 2.1882 0.94 1142 126 0.2328 0.3150 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.84 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 1282 REMARK 3 ANGLE : 1.051 1733 REMARK 3 CHIRALITY : 0.053 184 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 13.114 760 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 7BTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1300016451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-18 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9684 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.188 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 4KK3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM PHOSPHATE MONOBASIC, REMARK 280 100 MM SODIUM ACETATE TRIHYDRATE (PH 5.0), 10 MM CALCIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, 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 20.11800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.56250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.09800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.56250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.11800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.09800 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: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 LYS A 158 REMARK 465 GLU A 159 REMARK 465 LEU A 160 REMARK 465 SER A 161 REMARK 465 LEU A 162 REMARK 465 GLY A 163 REMARK 465 SER A 164 REMARK 465 LEU A 165 REMARK 465 GLU A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 63 CD CE NZ REMARK 470 THR A 101 OG1 CG2 REMARK 470 LYS A 118 CD CE NZ REMARK 470 LYS A 154 CD CE NZ 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 THR A 11 -16.51 -140.51 REMARK 500 CYS A 12 -77.49 -123.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 65 HIS A 66 -146.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 DBREF 7BTG A 1 164 UNP Q8ING6 Q8ING6_DROME 1 164 SEQADV 7BTG SER A 7 UNP Q8ING6 CYS 7 ENGINEERED MUTATION SEQADV 7BTG LEU A 165 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG GLU A 166 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 167 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 168 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 169 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 170 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 171 UNP Q8ING6 EXPRESSION TAG SEQADV 7BTG HIS A 172 UNP Q8ING6 EXPRESSION TAG SEQRES 1 A 172 MET LYS VAL LEU PHE VAL SER ILE GLY ASN THR CYS ARG SEQRES 2 A 172 SER PRO MET ALA GLU ALA ILE LEU LYS HIS LEU VAL VAL SEQRES 3 A 172 LYS ARG ASN LEU GLN ASP TRP TYR VAL ASP SER ALA GLY SEQRES 4 A 172 LEU ARG SER TRP ASN VAL GLY LEU GLU PRO GLN ALA ARG SEQRES 5 A 172 GLY GLN GLN LEU LEU LYS GLN HIS GLY LEU LYS THR ASN SEQRES 6 A 172 HIS LEU GLY ARG MET ILE SER ALA GLN ASP PHE TYR ASP SEQRES 7 A 172 PHE ASP TYR ILE PHE ALA MET ASP ASN SER ASN LEU LEU SEQRES 8 A 172 GLU LEU GLU HIS MET ALA ALA SER LEU THR PRO SER PRO SEQRES 9 A 172 THR CYS LYS ILE GLN LEU LEU GLY SER TYR ILE GLY ARG SEQRES 10 A 172 LYS GLU ASP GLU ILE ILE GLU ASP PRO TYR PHE ILE GLN SEQRES 11 A 172 GLY MET GLY GLY PHE ASN ALA ALA TYR LEU GLN ILE LEU SEQRES 12 A 172 GLU SER CYS GLU ARG PHE LEU GLN HIS TYR LYS SER ASP SEQRES 13 A 172 ASP LYS GLU LEU SER LEU GLY SER LEU GLU HIS HIS HIS SEQRES 14 A 172 HIS HIS HIS HET PO4 A 201 5 HET PO4 A 202 5 HET CL A 203 1 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 CL CL 1- FORMUL 5 HOH *37(H2 O) HELIX 1 AA1 CYS A 12 ARG A 28 1 17 HELIX 2 AA2 GLN A 50 GLN A 59 1 10 HELIX 3 AA3 SER A 72 PHE A 79 1 8 HELIX 4 AA4 ASP A 86 LEU A 100 1 15 HELIX 5 AA5 GLY A 112 ILE A 115 5 4 HELIX 6 AA6 ARG A 117 GLU A 121 5 5 HELIX 7 AA7 MET A 132 SER A 155 1 24 SHEET 1 AA1 4 TYR A 34 GLY A 39 0 SHEET 2 AA1 4 LYS A 2 SER A 7 1 N VAL A 3 O TYR A 34 SHEET 3 AA1 4 TYR A 81 ALA A 84 1 O PHE A 83 N VAL A 6 SHEET 4 AA1 4 LYS A 107 LEU A 110 1 O LYS A 107 N ILE A 82 CISPEP 1 GLN A 31 ASP A 32 0 -12.13 SITE 1 AC1 9 SER A 7 ILE A 8 GLY A 9 ASN A 10 SITE 2 AC1 9 THR A 11 CYS A 12 ARG A 13 HIS A 95 SITE 3 AC1 9 ASP A 125 SITE 1 AC2 6 GLU A 18 LYS A 22 ASP A 36 ASN A 65 SITE 2 AC2 6 HIS A 66 HOH A 315 SITE 1 AC3 1 HOH A 334 CRYST1 40.236 62.196 71.125 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 0.024853 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014060 0.00000