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- PDB-3jyo: Quinate dehydrogenase from Corynebacterium glutamicum in complex ... -

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Basic information

Entry
Database: PDB / ID: 3jyo
TitleQuinate dehydrogenase from Corynebacterium glutamicum in complex with NAD
ComponentsQuinate/shikimate dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme-cofactor complex / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Quinate/shikimate dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsHoeppner, A. / Niefind, K. / Schomburg, D.
CitationJournal: Biol.Chem. / Year: 2013
Title: Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity, and discrimination.
Authors: Hoppner, A. / Schomburg, D. / Niefind, K.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3882
Polymers29,7251
Non-polymers6631
Water7,945441
1
A: Quinate/shikimate dehydrogenase
hetero molecules

A: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7764
Polymers59,4492
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4620 Å2
ΔGint-23 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.45, 63.28, 36.34
Angle α, β, γ (deg.)90.00, 94.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein Quinate/shikimate dehydrogenase / NAD(+)-dependent quinate dehydrogenase / QDH / CglQDH


Mass: 29724.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC13032 / Gene: aroE, cg0504, Cgl0424 / Plasmid: pNHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9X5C9, quinate/shikimate dehydrogenase (NAD+), Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.6 M tri-sodium citrate, 0 up to 62.5 mM cobalt chloride, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1→10 Å / Num. all: 147745 / Num. obs: 137551 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.18 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 34
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.05 / Num. unique all: 14795 / Rsym value: 0.615 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2nlo

2nlo


Resolution: 1→10 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.604 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 6770 5 %Random
Rwork0.16326 ---
all0.16482 147745 --
obs0.16482 137551 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.18 Å2
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 44 441 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212342
X-RAY DIFFRACTIONr_bond_other_d0.0130.021482
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9893221
X-RAY DIFFRACTIONr_angle_other_deg3.39333656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56424.84597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67315376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5131515
X-RAY DIFFRACTIONr_chiral_restr0.1060.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022747
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02450
X-RAY DIFFRACTIONr_nbd_refined0.2540.2502
X-RAY DIFFRACTIONr_nbd_other0.230.21603
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21198
X-RAY DIFFRACTIONr_nbtor_other0.090.21200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3530.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.242
X-RAY DIFFRACTIONr_mcbond_it2.75961939
X-RAY DIFFRACTIONr_mcbond_other6.1186627
X-RAY DIFFRACTIONr_mcangle_it3.05692444
X-RAY DIFFRACTIONr_scbond_it3.8366908
X-RAY DIFFRACTIONr_scangle_it4.6899777
X-RAY DIFFRACTIONr_rigid_bond_restr3.07534542
X-RAY DIFFRACTIONr_sphericity_free9.913441
X-RAY DIFFRACTIONr_sphericity_bonded8.61233772
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1-1.040.6158011X-RAY DIFFRACTION2085.9
1.04-1.080.515X-RAY DIFFRACTION2094.7
1.08-1.130.339X-RAY DIFFRACTION2097.7
1.13-1.190.251X-RAY DIFFRACTION2097.8
1.19-1.260.194X-RAY DIFFRACTION2097.2
1.26-1.360.142X-RAY DIFFRACTION2096.5
1.36-1.490.102X-RAY DIFFRACTION2095.5
1.49-1.710.064X-RAY DIFFRACTION2094.1
1.71-2.150.046X-RAY DIFFRACTION2091.9
2.15-100.052X-RAY DIFFRACTION2080.1

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