HEADER LYASE 20-OCT-22 8EVK TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI DIHYDRONEOPTERIN ALDOLASE TITLE 2 (DHNA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRONEOPTERIN ALDOLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FULL-LENGTH; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI G27; SOURCE 3 ORGANISM_TAXID: 563041; SOURCE 4 STRAIN: G27; SOURCE 5 GENE: HPG27_1434; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJT250 KEYWDS INHIBITOR, COMPLEX, ALDOLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.X.SHAW,S.CHERRY,J.E.TROPEA,X.JI REVDAT 3 01-MAY-24 8EVK 1 JRNL REVDAT 2 25-OCT-23 8EVK 1 REMARK REVDAT 1 01-MAR-23 8EVK 0 JRNL AUTH G.X.SHAW,L.FAN,S.CHERRY,G.SHI,J.E.TROPEA,X.JI JRNL TITL STRUCTURE OF HELICOBACTER PYLORI DIHYDRONEOPTERIN ALDOLASE JRNL TITL 2 SUGGESTS A FRAGMENT-BASED STRATEGY FOR ISOZYME-SPECIFIC JRNL TITL 3 INHIBITOR DESIGN. JRNL REF CURR RES STRUCT BIOL V. 5 00095 2023 JRNL REFN ESSN 2665-928X JRNL PMID 36820301 JRNL DOI 10.1016/J.CRSTBI.2023.100095 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 21169 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1004 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 26.9000 - 2.8500 1.00 2953 149 0.1559 0.1852 REMARK 3 2 2.8500 - 2.2600 1.00 2928 151 0.2072 0.2469 REMARK 3 3 2.2600 - 1.9800 1.00 2926 146 0.2134 0.2572 REMARK 3 4 1.9800 - 1.8000 1.00 2897 144 0.2437 0.2707 REMARK 3 5 1.8000 - 1.6700 1.00 2926 144 0.2609 0.2897 REMARK 3 6 1.6700 - 1.5700 1.00 2896 142 0.2838 0.3026 REMARK 3 7 1.5700 - 1.4900 0.91 2639 128 0.3835 0.4461 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) : 0.243 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.63 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 1101 REMARK 3 ANGLE : 0.991 1491 REMARK 3 CHIRALITY : 0.082 170 REMARK 3 PLANARITY : 0.006 186 REMARK 3 DIHEDRAL : 14.658 439 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 8EVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21197 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.190 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: 2O90 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, NACL, ETC., PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.04050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.04050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.70200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.04050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.04050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.70200 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 34.04050 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 34.04050 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.70200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 34.04050 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 34.04050 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.70200 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 313 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 384 LIES ON A SPECIAL POSITION. 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 GLY A -2 REMARK 465 GLY A -1 REMARK 465 ASN A 115 REMARK 465 ASN A 116 REMARK 465 LEU A 117 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 67 -87.02 -82.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 8EVK A 1 117 UNP B5Z9C8 B5Z9C8_HELPG 1 117 SEQADV 8EVK GLY A -2 UNP B5Z9C8 EXPRESSION TAG SEQADV 8EVK GLY A -1 UNP B5Z9C8 EXPRESSION TAG SEQADV 8EVK GLY A 0 UNP B5Z9C8 EXPRESSION TAG SEQRES 1 A 120 GLY GLY GLY MET LYS THR LYS GLN GLY VAL HIS VAL HIS SEQRES 2 A 120 ASN LEU VAL PHE GLU THR ILE LEU GLY ILE LEU GLU PHE SEQRES 3 A 120 GLU ARG LEU LYS PRO GLN LYS ILE SER VAL ASP LEU ASP SEQRES 4 A 120 LEU PHE TYR THR GLN LEU PRO ASN LYS ALA TYR LEU ASP SEQRES 5 A 120 TYR ILE LYS ILE GLN GLU LEU ILE GLN LYS MET MET GLN SEQRES 6 A 120 GLU LYS GLN TYR LEU LEU ILE GLU ASP ALA LEU LYS ASP SEQRES 7 A 120 LEU SER GLN ILE LEU LYS THR ARG TYR LYS GLU ILE THR SEQRES 8 A 120 GLU LEU TYR LEU LYS ILE SER LYS LEU GLU ILE SER PRO SEQRES 9 A 120 ASP SER GLN VAL GLY ALA SER VAL LYS ILE CYS TYR GLU SEQRES 10 A 120 ASN ASN LEU HET PE0 A 201 12 HET EDO A 202 4 HETNAM PE0 PTERINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PE0 C6 H5 N5 O FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *134(H2 O) HELIX 1 AA1 LEU A 21 LYS A 27 5 7 HELIX 2 AA2 ASP A 49 GLN A 65 1 17 HELIX 3 AA3 LEU A 68 TYR A 84 1 17 SHEET 1 AA1 4 GLN A 5 THR A 16 0 SHEET 2 AA1 4 GLN A 29 TYR A 39 -1 O LEU A 35 N VAL A 9 SHEET 3 AA1 4 ILE A 87 LYS A 96 -1 O GLU A 89 N PHE A 38 SHEET 4 AA1 4 VAL A 105 CYS A 112 -1 O ALA A 107 N ILE A 94 CRYST1 68.081 68.081 57.404 90.00 90.00 90.00 I 4 8 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 0.014688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017420 0.00000