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

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Basic information

Entry
Database: PDB / ID: 3jyq
TitleQuinate dehydrogenase from Corynebacterium glutamicum in complex with shikimate and NADH
ComponentsQuinate/shikimate dehydrogenase
KeywordsOXIDOREDUCTASE / quinate dehyrogenase / ternary complex / shikimate / NADH / 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 3-dehydrogenase (NADP+) activity / shikimate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD+ binding
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 / Chem-SKM / Quinate/shikimate dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsHoeppner, A. / Schomburg, D. / Niefind, K.
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

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Assembly

Deposited unit
A: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5623
Polymers29,7251
Non-polymers8382
Water6,990388
1
A: Quinate/shikimate dehydrogenase
hetero molecules

A: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1246
Polymers59,4492
Non-polymers1,6754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5400 Å2
ΔGint-11 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.92, 63.39, 35.67
Angle α, β, γ (deg.)90.00, 94.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29724.580 Da / Num. of mol.: 1 / Fragment: QDH
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: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 24 % PEG 6000, 400 mM calcium chloride, 100 mM Tris/HCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. all: 92222 / Num. obs: 88626 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 18.36
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.33 / Num. unique all: 9155 / Rsym value: 0.362 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jyo

3jyo


Resolution: 1.16→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.17441 1781 -RANDOM
Rwork0.14921 ---
all0.1497 92222 --
obs0.1497 88626 96.1 %-
Displacement parametersBiso mean: 18.83 Å2
Refinement stepCycle: LAST / Resolution: 1.16→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 56 388 2519
LS refinement shell
Resolution (Å)Rfactor RfreeRefine-IDNum. reflection obs% reflection obs (%)
1.16-1.20.362X-RAY DIFFRACTION845092.3
1.2-1.250.296X-RAY DIFFRACTION861693.7
1.25-1.310.238X-RAY DIFFRACTION868694.2
1.31-1.380.188X-RAY DIFFRACTION869094.5
1.38-1.460.204X-RAY DIFFRACTION873895.2
1.46-1.570.244X-RAY DIFFRACTION887096.2
1.57-1.730.208X-RAY DIFFRACTION902397.8
1.73-1.980.159X-RAY DIFFRACTION915199.1
1.98-2.50.096X-RAY DIFFRACTION916799.1
2.5-300.071X-RAY DIFFRACTION923598.6

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