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- PDB-2hk8: Crystal structure of shikimate dehydrogenase from aquifex aeolicu... -

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Basic information

Entry
Database: PDB / ID: 2hk8
TitleCrystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 angstrom resolution
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate pathway / shikimate dehydrogenase / drug design
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily ...Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGan, J.H. / Prabakaran, P. / Gu, Y.J. / Andrykovitch, M. / Li, Y. / Liu, H.H. / Yan, H. / Ji, X.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
Authors: Gan, J. / Wu, Y. / Prabakaran, P. / Gu, Y. / Li, Y. / Andrykovitch, M. / Liu, H. / Gong, Y. / Yan, H. / Ji, X.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
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
Remark 999SEQUENCE Based on the electron density, especially the annealed omit maps, the authors believe ...SEQUENCE Based on the electron density, especially the annealed omit maps, the authors believe residue 195 in their structure is Glu and not Lys, residue 233 in their structure is Leu and not Phe, as it is in the UNP database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
E: Shikimate dehydrogenase
F: Shikimate dehydrogenase
G: Shikimate dehydrogenase
H: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)240,9058
Polymers240,9058
Non-polymers00
Water11,277626
1
A: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1131
Polymers30,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.361, 73.960, 192.107
Angle α, β, γ (deg.)94.64, 94.16, 91.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Shikimate dehydrogenase


Mass: 30113.145 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aroE / Plasmid: PET-17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O67049, shikimate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG20K, 0.1M MES (pH 6.4-6.6), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.05517 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2000
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05517 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 74160 / Num. obs: 74160 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.4 / % possible all: 44.8

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Processing

Software
NameVersionClassification
CNS1refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HK7

2hk7


Resolution: 2.35→28.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 37614.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3638 5.1 %RANDOM
Rwork0.214 ---
obs0.214 71656 84.2 %-
all-71656 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6362 Å2 / ksol: 0.329583 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å2-0.75 Å2-1.42 Å2
2--0.11 Å2-4.25 Å2
3----4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-30 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.35→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16797 0 0 626 17423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it3.082
X-RAY DIFFRACTIONc_scangle_it4.392.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 301 4.7 %
Rwork0.282 6142 -
obs--45.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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