HEADER HYDROLASE 31-MAY-21 7EYM TITLE CRYSTAL STRUCTURE OF VIBRIO CHOLERAE 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: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: PPNP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 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 7EYM 1 REMARK REVDAT 3 04-MAY-22 7EYM 1 JRNL REVDAT 2 23-FEB-22 7EYM 1 JRNL REVDAT 1 09-FEB-22 7EYM 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. 1.38 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 35447 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1784 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1431 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.44 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 7EYM 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_1300022525. 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 : 35454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.3330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.90100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.667 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 (%): 40.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% W/V REMARK 280 POLYETHYLENE GLYCOL 8,000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 55.92550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.62100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.62100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.96275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.62100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.62100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.88825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.62100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.62100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.96275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.62100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.62100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.88825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.92550 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: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 SER B 0 REMARK 465 ALA B 95 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 ASN A 75 O HOH A 101 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 153 DISTANCE = 5.86 ANGSTROMS DBREF1 7EYM A 1 95 UNP A0A0H6V0E6_VIBCL DBREF2 7EYM A A0A0H6V0E6 10 104 DBREF1 7EYM B 1 95 UNP A0A0H6V0E6_VIBCL DBREF2 7EYM B A0A0H6V0E6 10 104 SEQADV 7EYM SER A 0 UNP A0A0H6V0E EXPRESSION TAG SEQADV 7EYM SER B 0 UNP A0A0H6V0E EXPRESSION TAG SEQRES 1 A 96 SER MET ILE LYS GLU ASN VAL TYR PHE ASP GLY ASN VAL SEQRES 2 A 96 LYS SER LEU GLY PHE SER GLN GLN ASP GLY GLU SER THR SEQRES 3 A 96 VAL GLY VAL MET ALA PRO GLY GLN TYR THR PHE GLY THR SEQRES 4 A 96 GLY ALA PRO GLU ARG MET THR VAL VAL LYS GLY ALA LEU SEQRES 5 A 96 THR ILE LYS ARG VAL THR ASP ALA ASP TRP VAL THR PHE SEQRES 6 A 96 THR ALA GLY GLU ALA PHE GLU VAL ALA GLY ASN SER SER SEQRES 7 A 96 PHE ASP LEU GLN VAL GLU VAL ALA THR ALA TYR LEU CYS SEQRES 8 A 96 GLU PHE LEU PRO ALA SEQRES 1 B 96 SER MET ILE LYS GLU ASN VAL TYR PHE ASP GLY ASN VAL SEQRES 2 B 96 LYS SER LEU GLY PHE SER GLN GLN ASP GLY GLU SER THR SEQRES 3 B 96 VAL GLY VAL MET ALA PRO GLY GLN TYR THR PHE GLY THR SEQRES 4 B 96 GLY ALA PRO GLU ARG MET THR VAL VAL LYS GLY ALA LEU SEQRES 5 B 96 THR ILE LYS ARG VAL THR ASP ALA ASP TRP VAL THR PHE SEQRES 6 B 96 THR ALA GLY GLU ALA PHE GLU VAL ALA GLY ASN SER SER SEQRES 7 B 96 PHE ASP LEU GLN VAL GLU VAL ALA THR ALA TYR LEU CYS SEQRES 8 B 96 GLU PHE LEU PRO ALA FORMUL 3 HOH *110(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 LYS A 3 TYR A 7 0 SHEET 2 AA1 6 VAL A 12 GLN A 19 -1 O GLY A 16 N LYS A 3 SHEET 3 AA1 6 GLY A 22 MET A 29 -1 O GLY A 22 N GLN A 19 SHEET 4 AA1 6 THR A 86 PHE A 92 -1 O CYS A 90 N THR A 25 SHEET 5 AA1 6 GLU A 42 LYS A 48 -1 N THR A 45 O LEU A 89 SHEET 6 AA1 6 ALA A 69 VAL A 72 -1 O PHE A 70 N MET A 44 SHEET 1 AA2 4 GLY A 32 GLY A 37 0 SHEET 2 AA2 4 SER A 77 VAL A 82 -1 O VAL A 82 N GLY A 32 SHEET 3 AA2 4 ALA A 50 LYS A 54 -1 N THR A 52 O GLN A 81 SHEET 4 AA2 4 VAL A 62 THR A 65 -1 O VAL A 62 N ILE A 53 SHEET 1 AA3 6 LYS B 3 TYR B 7 0 SHEET 2 AA3 6 VAL B 12 GLN B 19 -1 O GLY B 16 N LYS B 3 SHEET 3 AA3 6 GLY B 22 MET B 29 -1 O VAL B 26 N LEU B 15 SHEET 4 AA3 6 THR B 86 PHE B 92 -1 O CYS B 90 N THR B 25 SHEET 5 AA3 6 GLU B 42 LYS B 48 -1 N ARG B 43 O GLU B 91 SHEET 6 AA3 6 ALA B 69 VAL B 72 -1 O PHE B 70 N MET B 44 SHEET 1 AA4 4 GLY B 32 GLY B 37 0 SHEET 2 AA4 4 SER B 77 VAL B 82 -1 O VAL B 82 N GLY B 32 SHEET 3 AA4 4 ALA B 50 LYS B 54 -1 N THR B 52 O GLN B 81 SHEET 4 AA4 4 VAL B 62 THR B 65 -1 O VAL B 62 N ILE B 53 CRYST1 55.242 55.242 111.851 90.00 90.00 90.00 P 41 21 2 16 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 0.018102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008940 0.00000