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- PDB-1hka: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE -

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Basic information

Entry
Database: PDB / ID: 1hka
Title6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
Components6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
KeywordsTRANSFERASE / PYROPHOSPHORYL TRANSFER / PYROPHOSPHOKINASE / KINASE / FOLATE / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN
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 / MAD / Resolution: 1.5 Å
AuthorsXiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X.
Citation
Journal: Structure Fold.Des. / 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.
#1: Journal: J.Bacteriol. / Year: 1992
Title: Cloning, Sequence Analysis, and Overexpression of Escherichia Coli Folk, the Gene Coding for 7,8-Dihydro-6-Hydroxymethylpterin-Pyrophosphokinase
Authors: Talarico, T.L. / Ray, P.H. / Dev, I.K. / Merrill, B.M. / Dallas, W.S.
#2: Journal: J.Bacteriol. / Year: 1991
Title: Purification and Partial Characterization of 7,8-Dihydro-6-Hydroxymethylpterin-Pyrophosphokinase and 7,8-Dihydropteroate Synthase from Escherichia Coli Mc4100
Authors: Talarico, T.L. / Dev, I.K. / Dallas, W.S. / Ferone, R. / Ray, P.H.
History
DepositionSep 29, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
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 / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE


Theoretical massNumber of molelcules
Total (without water)17,9671
Polymers17,9671
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.320, 51.980, 41.490
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE / HPPK


Mass: 17966.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FOLK / Production host: Escherichia coli (E. coli)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.66 Å3/Da / Density % sol: 26 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
230 %PEG40001reservoir
30.2 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9686, 0.9788, 0.9792, 0.9870
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97881
30.97921
40.9871
ReflectionResolution: 1.5→20 Å / Num. obs: 23352 / % possible obs: 95.8 % / Observed criterion σ(I): -0.5 / Redundancy: 5.65 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.06 / % possible all: 89.9
Reflection
*PLUS
Num. measured all: 132018
Reflection shell
*PLUS
% possible obs: 89.9 %

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Processing

Software
NameClassification
PHASESphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Num. parameters: 6235 / Num. restraintsaints: 5591 / Cross valid method: FREE R IN FIRST STAGE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI AND HOPE, J.APPL.CRYST. 28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
obs0.1818 -95.8 %-
all-22277 --
Rfree---RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1503
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 0 236 1555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(I): 2 / Rfactor all: 0.182 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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