HEADER TRANSFERASE 11-JUN-09 3HSZ TITLE CRYSTAL STRUCTURE OF E. COLI HPPK(F123A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPPK; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, 2- COMPND 5 AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE, 6- COMPND 6 HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K 12; SOURCE 5 GENE: B0142, FOIK, FOLK, JW0138; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS ALPHA BETA, ATP-BINDING, FOLATE BIOSYNTHESIS, KINASE, NUCLEOTIDE- KEYWDS 2 BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,Y.LI,H.YAN,X.JI REVDAT 5 06-SEP-23 3HSZ 1 REMARK REVDAT 4 30-AUG-23 3HSZ 1 AUTHOR JRNL REVDAT 3 13-OCT-21 3HSZ 1 REMARK SEQADV REVDAT 2 01-NOV-17 3HSZ 1 REMARK REVDAT 1 23-JUN-10 3HSZ 0 JRNL AUTH Y.LI,J.BLASZCZYK,X.JI,H.YAN JRNL TITL PTERIN-BINDING SITE MUTATION Y53A, N55A OR F123A AND JRNL TITL 2 ACTIVITY OF E. COLI HPPK JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.XIAO,G.SHI,X.CHEN,H.YAN,X.JI REMARK 1 TITL CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN REMARK 1 TITL 2 PYROPHOSPHOKINASE, A POTENTIAL TARGET FOR THE DEVELOPMENT OF REMARK 1 TITL 3 NOVEL ANTIMICROBIAL AGENTS REMARK 1 REF STRUCTURE V. 7 489 1999 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10378268 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 28203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.550 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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 21.9630 - 2.6740 1.00 3995 147 0.1490 0.1570 REMARK 3 2 2.6740 - 2.1230 1.00 3903 143 0.1340 0.1610 REMARK 3 3 2.1230 - 1.8550 1.00 3924 144 0.1240 0.2080 REMARK 3 4 1.8550 - 1.6850 1.00 3917 145 0.1380 0.2290 REMARK 3 5 1.6850 - 1.5650 0.99 3856 141 0.1510 0.2200 REMARK 3 6 1.5650 - 1.4720 0.99 3839 142 0.1750 0.2430 REMARK 3 7 1.4720 - 1.4000 0.97 3769 138 0.2130 0.2690 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 : 0.42 REMARK 3 B_SOL : 69.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.90500 REMARK 3 B22 (A**2) : 1.16200 REMARK 3 B33 (A**2) : -0.25700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.79300 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 1476 REMARK 3 ANGLE : 0.918 2019 REMARK 3 CHIRALITY : 0.065 219 REMARK 3 PLANARITY : 0.004 266 REMARK 3 DIHEDRAL : 16.816 559 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: THE STRUCTURE WAS REFINED FOR A TOTAL REMARK 3 OF 37 CYCLES, INCLUDING 4 CYCLES WITH CNS, 14 CYCLES WITH SHELX, REMARK 3 AND 19 CYCLES WITH PHENIX REMARK 4 REMARK 4 3HSZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00188 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28222 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 21.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0470 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1HKA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, MAGNESIUM REMARK 280 CHLORIDE, GLYCEROL, TRIS-HCL, PH 8.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 292K 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 26.03000 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 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 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 ASN A 10 -6.11 -170.74 REMARK 500 ALA A 12 -110.55 35.80 REMARK 500 PRO A 14 -15.33 -45.70 REMARK 500 ALA A 86 -17.41 66.33 REMARK 500 GLU A 87 63.63 -169.43 REMARK 500 ARG A 88 4.23 -60.98 REMARK 500 ARG A 88 4.23 -67.91 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 CL A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 194 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HKA RELATED DB: PDB REMARK 900 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE REMARK 900 RELATED ID: 3HSD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK(Y53A) REMARK 900 RELATED ID: 3HSG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK(Y53A) IN COMPLEX WITH MGAMPCPP REMARK 900 RELATED ID: 3HSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK(N55A) REMARK 900 RELATED ID: 3HT0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK(F123A) IN COMPLEX WITH MGAMPCPP DBREF 3HSZ A 1 158 UNP P26281 HPPK_ECOLI 2 159 SEQADV 3HSZ ALA A 123 UNP P26281 PHE 124 ENGINEERED MUTATION SEQRES 1 A 158 THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SER SEQRES 2 A 158 PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU GLY SEQRES 3 A 158 ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER PHE SEQRES 4 A 158 TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO ASP SEQRES 5 A 158 TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU ALA SEQRES 6 A 158 PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU LEU SEQRES 7 A 158 GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG TRP GLY PRO SEQRES 8 A 158 ARG THR LEU ASP LEU ASP ILE MET LEU PHE GLY ASN GLU SEQRES 9 A 158 VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR ASP SEQRES 10 A 158 MET LYS ASN ARG GLY ALA MET LEU TRP PRO LEU PHE GLU SEQRES 11 A 158 ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET LEU SEQRES 12 A 158 ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU ASN SEQRES 13 A 158 LYS TRP HET CL A 191 1 HET TRS A 192 16 HET TRS A 193 16 HET ACT A 194 4 HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM ACT ACETATE ION HETSYN TRS TRIS BUFFER FORMUL 2 CL CL 1- FORMUL 3 TRS 2(C4 H12 N O3 1+) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 HOH *213(H2 O) HELIX 1 1 PRO A 14 ASP A 27 1 14 HELIX 2 2 ALA A 65 GLY A 81 1 17 HELIX 3 3 ASP A 117 ASN A 120 5 4 HELIX 4 4 ARG A 121 ALA A 132 1 12 HELIX 5 5 MET A 142 ARG A 150 1 9 SHEET 1 A 4 SER A 31 VAL A 36 0 SHEET 2 A 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 A 4 VAL A 2 SER A 9 -1 N ALA A 3 O LEU A 60 SHEET 4 A 4 ASP A 95 PHE A 101 -1 O ASP A 95 N GLY A 8 SHEET 1 B 4 SER A 31 VAL A 36 0 SHEET 2 B 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 B 4 TYR A 40 THR A 42 -1 N THR A 42 O TYR A 53 SHEET 4 B 4 ASN A 156 LYS A 157 -1 O ASN A 156 N ARG A 41 SHEET 1 C 2 ILE A 106 ASN A 107 0 SHEET 2 C 2 THR A 112 VAL A 113 -1 O VAL A 113 N ILE A 106 CISPEP 1 VAL A 113 PRO A 114 0 -1.74 SITE 1 AC1 4 PRO A 114 LYS A 119 PRO A 138 ASP A 139 SITE 1 AC2 10 LEU A 70 ASP A 97 ILE A 98 LEU A 111 SITE 2 AC2 10 THR A 112 HIS A 115 TRS A 193 HOH A 204 SITE 3 AC2 10 HOH A 263 HOH A 375 SITE 1 AC3 11 GLU A 77 ARG A 92 ASP A 95 LEU A 96 SITE 2 AC3 11 ASP A 97 HIS A 148 TRS A 192 HOH A 302 SITE 3 AC3 11 HOH A 318 HOH A 351 HOH A 412 SITE 1 AC4 4 LEU A 11 ALA A 12 SER A 13 PRO A 14 CRYST1 36.150 52.060 41.390 90.00 110.54 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 0.027664 0.000000 0.010367 0.00000 SCALE2 0.000000 0.019210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025802 0.00000