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- PDB-1sfj: 2.4A Crystal structure of Staphylococcus aureus type I 3-dehydroq... -

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Basic information

Entry
Database: PDB / ID: 1sfj
Title2.4A Crystal structure of Staphylococcus aureus type I 3-dehydroquinase, with 3-dehydroquinate bound
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-dehydroquinase / enzyme turnover / shikimate pathway / 3-dehydroquinate
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-DEHYDROSHIKIMATE / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNichols, C.E. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Proteins / Year: 2004
Title: Crystal structures of Staphylococcus aureus type I dehydroquinase from enzyme turnover experiments
Authors: Nichols, C.E. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5064
Polymers54,1582
Non-polymers3482
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-6 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.580, 76.580, 172.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe crystallographic and biological dimers are equivalent and the asymetric unit contains one dimer.

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Components

#1: Protein 3-dehydroquinate dehydratase / / 3-dehydroquinase / Type I DHQase


Mass: 27079.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MRSA252 / Gene: aroD / Plasmid: pRF88 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6GII7, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-DHK / 3-DEHYDROSHIKIMATE / 3-Dehydroshikimic acid


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 277 K / pH: 8
Details: PEG 8000, TRIS, potassium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9333
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 19857 / % possible obs: 94.8 % / Observed criterion σ(I): -1.5 / Redundancy: 3.9 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2033 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFE

1qfe


Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1556 -RANDOM
Rwork0.19 ---
obs0.19 19857 95.5 %-
all-20946 --
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-1.4 Å22.8 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 22 269 3957
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.323 175 -
Rwork0.272 2013 -
obs--99.5 %

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