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- PDB-3hsz: Crystal structure of E. coli HPPK(F123A) -

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Basic information

Entry
Database: PDB / ID: 3hsz
TitleCrystal structure of E. coli HPPK(F123A)
ComponentsHPPK
KeywordsTRANSFERASE / alpha beta / ATP-binding / Folate biosynthesis / Kinase / Nucleotide-binding
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsBlaszczyk, J. / Li, Y. / Yan, H. / Ji, X.
Citation
Journal: To be Published
Title: Pterin-binding site mutation Y53A, N55A or F123A and activity of E. coli HPPK
Authors: Li, Y. / Blaszczyk, J. / Ji, X. / Yan, H.
#1: Journal: Structure / Year: 1999
Title: Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents
Authors: Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HPPK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2295
Polymers17,8901
Non-polymers3394
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.15, 52.06, 41.39
Angle α, β, γ (deg.)90.00, 110.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HPPK / 7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / 2-amino-4-hydroxy-6- ...7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK


Mass: 17890.438 Da / Num. of mol.: 1 / Mutation: F124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K 12 / Gene: b0142, foIK, folK, JW0138 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 4000, Sodium acetate, Magnesium chloride, Glycerol, Tris-HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.00188 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2000 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00188 Å / Relative weight: 1
ReflectionResolution: 1.4→21.96 Å / Num. all: 28222 / Num. obs: 28222 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 14.35 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.011 / Net I/σ(I): 20.047
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2762 / Χ2: 1.137 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HKA

1hka


Resolution: 1.4→21.96 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.18
Isotropic thermal model: Anisotropic B factors for non-H atoms of full occupancy
Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED FOR A TOTAL OF 37 CYCLES, INCLUDING 4 CYCLES WITH CNS, 14 CYCLES WITH SHELX, AND 19 CYCLES WITH PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1000 3.55 %Random
Rwork0.15 ---
all0.152 28203 --
obs0.152 28203 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.635 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso max: 83.26 Å2 / Biso mean: 22.388 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.905 Å2-0 Å20.793 Å2
2--1.162 Å20 Å2
3----0.257 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 21 213 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041476
X-RAY DIFFRACTIONf_angle_d0.9182019
X-RAY DIFFRACTIONf_chiral_restr0.065219
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d16.816559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.4-1.4720.2691380.21337693907390797
1.472-1.5650.2431420.17538393981398199
1.565-1.6850.221410.15138563997399799
1.685-1.8550.2291450.138391740624062100
1.855-2.1230.2081440.124392440684068100
2.123-2.6740.1611430.134390340464046100
2.674-21.9630.1571470.149399541424142100

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