HEADER HYDROLASE 21-MAR-21 7EF7 TITLE CRYSTAL STRUCTURE OF XANTHOSINE MONOPHOSPHATE PHOSPHATASE COMPLEX WITH TITLE 2 XMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: AT2G32150/F22D22.10; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-250; COMPND 5 SYNONYM: HALOACID DEHALOGENASE-LIKE HYDROLASE (HAD) SUPERFAMILY COMPND 6 PROTEIN,PUTATIVE HYDROLASE; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT2G32150, AT2G32150/F22D22.10, F22D22.10, F22D22_10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS XMPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YANG,S.RHEE REVDAT 3 29-NOV-23 7EF7 1 REMARK REVDAT 2 18-MAY-22 7EF7 1 JRNL REVDAT 1 03-NOV-21 7EF7 0 JRNL AUTH K.J.HEINEMANN,S.Y.YANG,H.STRAUBE,N.MEDINA-ESCOBAR, JRNL AUTH 2 M.VARBANOVA-HERDE,M.HERDE,S.RHEE,C.P.WITTE JRNL TITL INITIATION OF CYTOSOLIC PLANT PURINE NUCLEOTIDE CATABOLISM JRNL TITL 2 INVOLVES A MONOSPECIFIC XANTHOSINE MONOPHOSPHATE JRNL TITL 3 PHOSPHATASE. JRNL REF NAT COMMUN V. 12 6846 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34824243 JRNL DOI 10.1038/S41467-021-27152-4 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 37810 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1577 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 25.4020 - 3.3337 0.94 3204 151 0.1713 0.1917 REMARK 3 2 3.3337 - 2.6470 1.00 3381 147 0.2137 0.2235 REMARK 3 3 2.6470 - 2.3126 1.00 3347 156 0.2093 0.2594 REMARK 3 4 2.3126 - 2.1013 1.00 3322 152 0.1982 0.2501 REMARK 3 5 2.1013 - 1.9507 1.00 3359 139 0.2060 0.2496 REMARK 3 6 1.9507 - 1.8358 1.00 3340 136 0.2219 0.2834 REMARK 3 7 1.8358 - 1.7439 1.00 3346 138 0.2492 0.2779 REMARK 3 8 1.7439 - 1.6680 1.00 3312 146 0.2794 0.3236 REMARK 3 9 1.6680 - 1.6038 0.99 3341 138 0.3319 0.3054 REMARK 3 10 1.6038 - 1.5484 0.97 3185 145 0.3622 0.4116 REMARK 3 11 1.5484 - 1.5000 0.93 3096 129 0.3986 0.4177 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.290 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 : 0.009 1898 REMARK 3 ANGLE : 1.169 2580 REMARK 3 CHIRALITY : 0.051 301 REMARK 3 PLANARITY : 0.006 326 REMARK 3 DIHEDRAL : 12.588 688 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 7EF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-18 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 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 : 37816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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: 7EF6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.0) 18%(W/V) REMARK 280 PEG12000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.38950 REMARK 290 SMTRY3 2 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: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 239 REMARK 465 VAL A 240 REMARK 465 GLY A 241 REMARK 465 GLY A 242 REMARK 465 GLU A 243 REMARK 465 ARG A 244 REMARK 465 ILE A 245 REMARK 465 ARG A 246 REMARK 465 ARG A 247 REMARK 465 SER A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 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 SER A 4 OG REMARK 470 ARG A 204 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 227 CG CD OE1 OE2 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 LEU A 13 -69.57 -105.84 REMARK 500 SER A 60 130.70 -175.56 REMARK 500 CYS A 136 -169.30 -126.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 14 O REMARK 620 2 ASP A 184 OD1 73.0 REMARK 620 3 ASP A 184 OD2 89.1 52.1 REMARK 620 4 XMP A 302 O3P 90.1 119.9 171.8 REMARK 620 N 1 2 3 DBREF 7EF7 A 1 250 UNP Q9SKY5 Q9SKY5_ARATH 1 250 SEQADV 7EF7 ALA A 12 UNP Q9SKY5 ASP 12 ENGINEERED MUTATION SEQRES 1 A 250 MET ASP PHE SER PRO ILE ASN CYS LEU ILE PHE ALA LEU SEQRES 2 A 250 ASP ASP THR LEU TYR PRO LEU LYS THR GLY ILE ALA PRO SEQRES 3 A 250 ALA VAL LYS LYS ASN ILE ASP ASP PHE LEU VAL GLU LYS SEQRES 4 A 250 PHE GLY PHE SER GLU SER LYS ALA SER SER LEU ARG VAL SEQRES 5 A 250 GLU LEU PHE LYS THR TYR GLY SER THR LEU ALA GLY LEU SEQRES 6 A 250 ARG ALA LEU GLY HIS ASP VAL HIS PRO ASP GLU TYR HIS SEQRES 7 A 250 SER PHE VAL HIS GLY ARG LEU PRO TYR GLY SER ILE GLU SEQRES 8 A 250 PRO ASN ASN LYS LEU ARG ASN LEU LEU ASN LYS ILE LYS SEQRES 9 A 250 GLN ARG LYS ILE ILE PHE THR ASN SER ASP LYS ASN HIS SEQRES 10 A 250 ALA VAL LYS VAL LEU LYS LYS LEU GLY LEU GLU ASP CYS SEQRES 11 A 250 PHE GLU GLU MET ILE CYS PHE GLU THR MET ASN PRO ASN SEQRES 12 A 250 LEU PHE GLY SER THR THR ARG PRO ASP GLU TYR PRO VAL SEQRES 13 A 250 VAL LEU LYS PRO SER LEU THR ALA MET ASP ILE CYS ILE SEQRES 14 A 250 ARG VAL ALA ASN VAL ASP PRO ARG ARG THR VAL PHE LEU SEQRES 15 A 250 ASP ASP ASN ILE HIS ASN ILE THR ALA GLY LYS SER VAL SEQRES 16 A 250 GLY LEU ARG THR ILE LEU VAL GLY ARG ALA GLU LYS THR SEQRES 17 A 250 LYS ASP ALA ASP TYR ALA VAL GLU THR VAL THR GLU ILE SEQRES 18 A 250 ALA THR ALA VAL PRO GLU ILE TRP ALA THR ALA THR ALA SEQRES 19 A 250 THR GLY GLY PHE ASP VAL GLY GLY GLU ARG ILE ARG ARG SEQRES 20 A 250 SER LYS SER HET MG A 301 1 HET XMP A 302 24 HETNAM MG MAGNESIUM ION HETNAM XMP XANTHOSINE-5'-MONOPHOSPHATE HETSYN XMP 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE FORMUL 2 MG MG 2+ FORMUL 3 XMP C10 H14 N4 O9 P 1+ FORMUL 4 HOH *80(H2 O) HELIX 1 AA1 PRO A 19 THR A 22 5 4 HELIX 2 AA2 GLY A 23 GLY A 41 1 19 HELIX 3 AA3 SER A 43 GLY A 59 1 17 HELIX 4 AA4 SER A 60 LEU A 68 1 9 HELIX 5 AA5 HIS A 73 HIS A 82 1 10 HELIX 6 AA6 PRO A 86 ILE A 90 5 5 HELIX 7 AA7 ASN A 93 ILE A 103 1 11 HELIX 8 AA8 ASP A 114 GLY A 126 1 13 HELIX 9 AA9 CYS A 136 ASN A 141 1 6 HELIX 10 AB1 PRO A 142 PHE A 145 5 4 HELIX 11 AB2 SER A 161 ASN A 173 1 13 HELIX 12 AB3 ASP A 175 ARG A 177 5 3 HELIX 13 AB4 ASN A 185 VAL A 195 1 11 HELIX 14 AB5 THR A 217 THR A 219 5 3 HELIX 15 AB6 GLU A 220 VAL A 225 1 6 HELIX 16 AB7 PRO A 226 ALA A 230 5 5 SHEET 1 AA1 6 GLU A 133 ILE A 135 0 SHEET 2 AA1 6 ARG A 106 PHE A 110 1 N ILE A 109 O ILE A 135 SHEET 3 AA1 6 CYS A 8 PHE A 11 1 N PHE A 11 O ILE A 108 SHEET 4 AA1 6 THR A 179 ASP A 183 1 O LEU A 182 N ILE A 10 SHEET 5 AA1 6 ARG A 198 VAL A 202 1 O ILE A 200 N PHE A 181 SHEET 6 AA1 6 TYR A 213 VAL A 215 1 O TYR A 213 N LEU A 201 LINK O ASP A 14 MG MG A 301 1555 1555 2.39 LINK OD1 ASP A 184 MG MG A 301 1555 1555 2.51 LINK OD2 ASP A 184 MG MG A 301 1555 1555 2.57 LINK MG MG A 301 O3P XMP A 302 1555 1555 2.15 CISPEP 1 LYS A 159 PRO A 160 0 9.68 CRYST1 37.670 56.779 56.958 90.00 92.92 90.00 P 1 21 1 2 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 0.026546 0.000000 0.001356 0.00000 SCALE2 0.000000 0.017612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017580 0.00000