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- PDB-3ud5: Crystal structure of E. coli HPPK in complex with bisubstrate ana... -

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Basic information

Entry
Database: PDB / ID: 3ud5
TitleCrystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1A
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Alpha Beta / Kinase / ATP Binding / 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-J1A / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsShaw, G. / Shi, G. / Ji, X.
Citation
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.
#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.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 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)18,6754
Polymers17,9671
Non-polymers7093
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.92, 52.84, 36.76
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number5
Space group name H-MC121

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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-J1A / 5'-S-[1-(2-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine


Mass: 584.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N12O4S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.5 % / Number: 66903 / Rmerge(I) obs: 0.089 / Χ2: 0.92 / D res high: 1.9 Å / D res low: 30 Å / Num. obs: 10236 / % possible obs: 87
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
1.91.9761.710.320.9045.3
1.972.0567.310.2520.9195.8
2.052.1475.410.2190.7556.2
2.142.2581.710.1840.8956.3
2.252.3991.510.1610.9656.5
2.392.5897.810.1390.966.8
2.582.8499.710.1160.9497.1
2.843.2599.710.0870.997.1
3.254.0997.110.0690.866.8
4.093097.710.0660.9556.6
ReflectionResolution: 1.9→30 Å / Num. all: 10236 / Num. obs: 10236 / % possible obs: 87 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.9-2.020.2891230163.3
2.02-2.170.2141465174.8
2.17-2.390.1661725188.5
2.39-2.740.131914198.5
2.74-3.450.0881958199.5
3.45-300.0671944197.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1EQM

1eqm


Resolution: 2→29.841 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 824 8.91 %Random
Rwork0.1599 ---
obs0.164 9252 90.71 %-
all-9252 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.426 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 99.63 Å2 / Biso mean: 31.0252 Å2 / Biso min: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1-26.0604 Å2-0 Å29.1949 Å2
2---7.7768 Å2-0 Å2
3----3.2667 Å2
Refinement stepCycle: LAST / Resolution: 2→29.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 49 106 1422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121415
X-RAY DIFFRACTIONf_angle_d1.3021936
X-RAY DIFFRACTIONf_chiral_restr0.076211
X-RAY DIFFRACTIONf_plane_restr0.008251
X-RAY DIFFRACTIONf_dihedral_angle_d15.858537
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 (%)
2-2.12540.26171070.164310961203120372
2.1254-2.28940.22651260.165912881414141482
2.2894-2.51970.24221400.160614351575157594
2.5197-2.88410.22551510.1488153916901690100
2.8841-3.63260.19121500.147215361686168699
3.6326-29.84410.17911500.169415341684168497

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