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- PDB-2nlo: Crystal Structure of the Quinate Dehydrogenase from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 2nlo
TitleCrystal Structure of the Quinate Dehydrogenase from Corynebacterium glutamicum
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / quinate / shikimate / rossmann fold
Function / homology
Function and homology information


quinate/shikimate dehydrogenase (NAD+) / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / NAD+ binding / amino acid biosynthetic process ...quinate/shikimate dehydrogenase (NAD+) / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / NAD+ binding / amino acid biosynthetic process / NADP binding / cytosol
Similarity search - Function
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 ...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
Quinate/shikimate dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsSchoepe, J. / Niefind, K. / Schomburg, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: 1.6 A structure of an NAD(+)-dependent quinate dehydrogenase from Corynebacterium glutamicum
Authors: Schoepe, J. / Niefind, K. / Schomburg, D.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionNov 14, 2006ID: 2EZ3
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.5Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0022
Polymers31,9101
Non-polymers921
Water4,594255
1
A: Shikimate dehydrogenase
hetero molecules

A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0044
Polymers63,8202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2940 Å2
ΔGint-9 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.784, 63.021, 35.527
Angle α, β, γ (deg.)90.00, 92.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Shikimate dehydrogenase / E.C.1.1.1.25 / Shikimate 5-dehydrogenase


Mass: 31909.910 Da / Num. of mol.: 1 / Mutation: N-tagged wild type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: ATCC13032 / Gene: Cgl0424 / Plasmid: pETNHis / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9X5C9, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.6→7.99 Å / Num. obs: 29404

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NVT

1nvt


Resolution: 1.643→7.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.95 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16543 1526 4.9 %RANDOM
Rwork0.14812 ---
obs0.149 29404 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.04 Å2
2---0.18 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.643→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 6 255 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212101
X-RAY DIFFRACTIONr_bond_other_d0.0010.021343
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9672857
X-RAY DIFFRACTIONr_angle_other_deg0.84533293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94224.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53615332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined0.210.2441
X-RAY DIFFRACTIONr_nbd_other0.1950.21480
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21074
X-RAY DIFFRACTIONr_nbtor_other0.0850.21119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.39161770
X-RAY DIFFRACTIONr_mcbond_other0.5966583
X-RAY DIFFRACTIONr_mcangle_it2.62692206
X-RAY DIFFRACTIONr_scbond_it3.0226787
X-RAY DIFFRACTIONr_scangle_it4.1629651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.643→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 87 -
Rwork0.26 1932 -
obs--89.14 %

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