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- PDB-3kug: Crystal structure of E. coli HPPK(H115A) -

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Basic information

Entry
Database: PDB / ID: 3kug
TitleCrystal structure of E. coli HPPK(H115A)
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
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
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsBlaszczyk, J. / Li, Y. / Yan, H. / Ji, X.
Citation
Journal: To be Published
Title: Roles of residues E77 and H115 in 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
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)17,8991
Polymers17,8991
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.10, 47.00, 42.20
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17899.465 Da / Num. of mol.: 1 / Mutation: H116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.82 Å3/Da / Density % sol: 32.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 4000, Sodium acetate, Magnesium chloride, Tris-HCl, Imidazole, 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: 0.97125 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2001 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97125 Å / Relative weight: 1
ReflectionResolution: 1.996→30 Å / Num. all: 8672 / Num. obs: 8672 / % possible obs: 98.1 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 0.183 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.005 / Net I/σ(I): 8.4
Reflection shellResolution: 1.996→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.5 / Num. unique all: 817 / Χ2: 0.965 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKA

1hka


Resolution: 1.996→23.5 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.32 / Isotropic thermal model: Isotrooic / Cross valid method: THROUGHOUT / σ(F): 1.43 / Stereochemistry target values: ML
Details: The structure was refined for a total of 21 cycles, including 8 cycles with CNS, 6 cycles with SHELXL, and 7 cycles with PHENIX.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 871 10.05 %Random
Rwork0.192 ---
all0.197 8664 --
obs0.197 8664 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.194 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 62.7 Å2 / Biso mean: 19.197 Å2 / Biso min: 5.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.105 Å20 Å2-0.53 Å2
2--0.679 Å2-0 Å2
3---1.426 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.996→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 0 105 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051311
X-RAY DIFFRACTIONf_angle_d0.6311790
X-RAY DIFFRACTIONf_chiral_restr0.038200
X-RAY DIFFRACTIONf_plane_restr0.004237
X-RAY DIFFRACTIONf_dihedral_angle_d14.485491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.996-2.1210.2941400.22512601400140095
2.121-2.2850.2781500.20512741424142498
2.285-2.5150.3011410.212881429142998
2.515-2.8780.2541460.213071453145398
2.878-3.6240.2071470.18913091456145699
3.624-23.5010.1771470.17113551502150299

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