HEADER HYDROLASE 31-MAY-21 7EYL TITLE CRYSTAL STRUCTURE OF SALMONELLA ENTERICA PPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIMIDINE/PURINE NUCLEOSIDE PHOSPHORYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ADENOSINE PHOSPHORYLASE,CYTIDINE PHOSPHORYLASE,GUANOSINE COMPND 5 PHOSPHORYLASE,INOSINE PHOSPHORYLASE,THYMIDINE PHOSPHORYLASE,URIDINE COMPND 6 PHOSPHORYLASE,XANTHOSINE PHOSPHORYLASE; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA; SOURCE 3 ORGANISM_COMMON: SALMONELLA CHOLERAESUIS; SOURCE 4 ORGANISM_TAXID: 28901; SOURCE 5 GENE: PPNP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PYRIMIDINE, PURINE, NUCLEOSIDE PHOSPHORYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.WEN,B.X.WU REVDAT 4 29-NOV-23 7EYL 1 REMARK REVDAT 3 04-MAY-22 7EYL 1 JRNL REVDAT 2 23-FEB-22 7EYL 1 JRNL REVDAT 1 09-FEB-22 7EYL 0 JRNL AUTH Y.WEN,X.LI,W.GUO,B.WU JRNL TITL CRYSTAL STRUCTURES OF A NEW CLASS OF PYRIMIDINE/PURINE JRNL TITL 2 NUCLEOSIDE PHOSPHORYLASE REVEALED A CUPIN FOLD. JRNL REF PROTEINS V. 90 1233 2022 JRNL REFN ESSN 1097-0134 JRNL PMID 35094440 JRNL DOI 10.1002/PROT.26309 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC V1.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 51507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2611 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1442 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.69 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7EYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-21 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8240 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.824 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: 7EYJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.62833 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.25667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 HOH A 101 O HOH A 164 2.09 REMARK 500 NZ LYS B 63 O HOH B 101 2.19 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 ALA A 40 -86.94 -98.92 REMARK 500 SER A 77 -156.64 -149.31 REMARK 500 ALA B 40 -86.70 -98.87 REMARK 500 SER B 77 -156.22 -149.00 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7EYL A 1 94 UNP A0A0W4AVI3_SALER DBREF2 7EYL A A0A0W4AVI3 1 94 DBREF1 7EYL B 1 94 UNP A0A0W4AVI3_SALER DBREF2 7EYL B A0A0W4AVI3 1 94 SEQADV 7EYL SER A 0 UNP A0A0W4AVI EXPRESSION TAG SEQADV 7EYL SER B 0 UNP A0A0W4AVI EXPRESSION TAG SEQRES 1 A 95 SER MET LEU GLN SER ASN GLU TYR PHE SER GLY LYS VAL SEQRES 2 A 95 LYS SER ILE GLY PHE THR SER SER SER THR GLY ARG ALA SEQRES 3 A 95 SER VAL GLY VAL MET ALA GLU GLY GLU TYR THR PHE GLY SEQRES 4 A 95 THR ALA GLU PRO GLU GLU MET THR VAL VAL SER GLY ALA SEQRES 5 A 95 LEU LYS VAL LEU LEU PRO GLY THR VAL GLU TRP LYS VAL SEQRES 6 A 95 TYR THR ALA GLY GLU VAL PHE ASN VAL PRO GLY HIS SER SEQRES 7 A 95 GLU PHE HIS LEU GLN VAL ALA GLU PRO ALA SER TYR LEU SEQRES 8 A 95 CYS ARG TYR LEU SEQRES 1 B 95 SER MET LEU GLN SER ASN GLU TYR PHE SER GLY LYS VAL SEQRES 2 B 95 LYS SER ILE GLY PHE THR SER SER SER THR GLY ARG ALA SEQRES 3 B 95 SER VAL GLY VAL MET ALA GLU GLY GLU TYR THR PHE GLY SEQRES 4 B 95 THR ALA GLU PRO GLU GLU MET THR VAL VAL SER GLY ALA SEQRES 5 B 95 LEU LYS VAL LEU LEU PRO GLY THR VAL GLU TRP LYS VAL SEQRES 6 B 95 TYR THR ALA GLY GLU VAL PHE ASN VAL PRO GLY HIS SER SEQRES 7 B 95 GLU PHE HIS LEU GLN VAL ALA GLU PRO ALA SER TYR LEU SEQRES 8 B 95 CYS ARG TYR LEU FORMUL 3 HOH *200(H2 O) HELIX 1 AA1 PHE A 8 GLY A 10 5 3 HELIX 2 AA2 PHE B 8 GLY B 10 5 3 SHEET 1 AA1 6 GLN A 3 TYR A 7 0 SHEET 2 AA1 6 VAL A 12 SER A 19 -1 O GLY A 16 N GLN A 3 SHEET 3 AA1 6 GLY A 23 MET A 30 -1 O ALA A 25 N PHE A 17 SHEET 4 AA1 6 ALA A 87 TYR A 93 -1 O CYS A 91 N SER A 26 SHEET 5 AA1 6 GLU A 43 SER A 49 -1 N THR A 46 O LEU A 90 SHEET 6 AA1 6 VAL A 70 VAL A 73 -1 O PHE A 71 N MET A 45 SHEET 1 AA2 4 GLY A 33 THR A 39 0 SHEET 2 AA2 4 SER A 77 VAL A 83 -1 O LEU A 81 N TYR A 35 SHEET 3 AA2 4 ALA A 51 LEU A 55 -1 N LYS A 53 O GLN A 82 SHEET 4 AA2 4 LYS A 63 THR A 66 -1 O LYS A 63 N VAL A 54 SHEET 1 AA3 6 GLN B 3 TYR B 7 0 SHEET 2 AA3 6 VAL B 12 SER B 19 -1 O GLY B 16 N GLN B 3 SHEET 3 AA3 6 GLY B 23 MET B 30 -1 O ALA B 25 N PHE B 17 SHEET 4 AA3 6 ALA B 87 TYR B 93 -1 O CYS B 91 N SER B 26 SHEET 5 AA3 6 GLU B 43 SER B 49 -1 N THR B 46 O LEU B 90 SHEET 6 AA3 6 VAL B 70 VAL B 73 -1 O PHE B 71 N MET B 45 SHEET 1 AA4 4 GLY B 33 THR B 39 0 SHEET 2 AA4 4 SER B 77 VAL B 83 -1 O LEU B 81 N TYR B 35 SHEET 3 AA4 4 ALA B 51 LEU B 55 -1 N LYS B 53 O GLN B 82 SHEET 4 AA4 4 LYS B 63 THR B 66 -1 O LYS B 63 N VAL B 54 CRYST1 34.571 34.571 124.885 90.00 90.00 120.00 P 31 6 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 0.028926 0.016700 0.000000 0.00000 SCALE2 0.000000 0.033401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008007 0.00000