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- PDB-3phg: Crystal structure of the Shikimate 5-Dehydrogenase (aroE) from He... -

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Basic information

Entry
Database: PDB / ID: 3phg
TitleCrystal structure of the Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate dehydrogenase / shikimate pathway / Helicobacter pylori / alpha/beta domain / Rossmann fold
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase / Shikimate dehydrogenase family / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsCheng, W.C. / Lin, S.C. / Wang, W.C.
CitationJournal: To be Published
Title: Crystal structure of the Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori
Authors: Cheng, W.C. / Lin, S.C. / Wang, W.C.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,2782
Polymers60,2782
Non-polymers00
Water6,395355
1
A: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1391
Polymers30,1391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)30,1391
Polymers30,1391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.328, 46.181, 118.702
Angle α, β, γ (deg.)90.00, 99.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shikimate dehydrogenase


Mass: 30138.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: aroE, HP_1249 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P56119, shikimate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0941.23
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium chloride, 35% PEG 3350, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11102
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONSPring-8 BL12B220.978998
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJan 17, 2009
ADSC QUANTUM 210r2CCDJul 2, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9789981
ReflectionResolution: 1.57→30 Å / Num. obs: 66787 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 19.8
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.39 / Num. unique all: 6065 / Rsym value: 0.448 / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.57→23.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23967 3377 5.1 %RANDOM
Rwork0.19958 ---
obs0.20162 63407 98.29 %-
all-66787 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.956 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å2-0.07 Å2
2---0.87 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.57→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 0 355 4374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224108
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9845528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.624.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50615736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3761510
X-RAY DIFFRACTIONr_chiral_restr0.110.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213029
X-RAY DIFFRACTIONr_mcbond_it1.0541.52544
X-RAY DIFFRACTIONr_mcangle_it1.91524057
X-RAY DIFFRACTIONr_scbond_it3.02331564
X-RAY DIFFRACTIONr_scangle_it4.7864.51471
LS refinement shellResolution: 1.571→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 221 -
Rwork0.261 4095 -
obs--86.23 %

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