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- PDB-4f7v: Crystal structure of E. coli HPPK in complex with bisubstrate ana... -

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Basic information

Entry
Database: PDB / ID: 4f7v
TitleCrystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1D (HP26)
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha beta / pyrophosphokinase / pyrophosphoryl transfer / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-J1D / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsShaw, G. / Shi, G. / Ji, X.
Citation
Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New lead exhibits a distinct binding mode.
Authors: Shi, G. / Shaw, G. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
#1: Journal: J.Med.Chem. / Year: 2001
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H.
#2: Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
Authors: Shi, G. / Shaw, G. / Liang, Y.H. / Subburaman, P. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6012
Polymers17,9671
Non-polymers6351
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.118, 70.581, 36.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

21A-470-

HOH

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Components

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin- ...6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin-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) / 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: Chemical ChemComp-J1D / 5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine


Mass: 634.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N12O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, NaCl, HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. all: 14746 / Num. obs: 14746 / % possible obs: 89 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 16.58 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.67-1.732.50.4111.85802149.1
1.73-1.83.10.3772.421054165.8
1.8-1.8840.3253.511361183.1
1.88-1.984.60.2485.3114970.99892.5
1.98-2.15.10.1927.1116241.00299
2.1-2.275.30.14510.0316311.00199.5
2.27-2.495.50.10813.8916350.99899.6
2.49-2.865.50.09416.21658199.8
2.86-3.65.70.08317.4717000.99999.8
3.6-305.60.04928.617841.00199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UDV

3udv


Resolution: 1.73→27.569 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 940 6.8 %Random
Rwork0.1722 ---
obs0.1755 13829 93.57 %-
all-13829 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.99 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 97.75 Å2 / Biso mean: 20.485 Å2 / Biso min: 3.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→27.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 44 171 1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121372
X-RAY DIFFRACTIONf_angle_d1.3791881
X-RAY DIFFRACTIONf_chiral_restr0.076206
X-RAY DIFFRACTIONf_plane_restr0.008242
X-RAY DIFFRACTIONf_dihedral_angle_d15.384533
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 (%)
1.73-1.82130.349970.27713221419141970
1.8213-1.93540.29591230.236616931816181688
1.9354-2.08480.25121390.200618992038203898
2.0848-2.29450.24961410.182919472088208899
2.2945-2.62630.22611420.1734194520872087100
2.6263-3.30790.23551470.1589200521522152100
3.3079-27.57260.16861510.1438207822292229100

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