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- PDB-3zok: Structure of 3-Dehydroquinate Synthase from Actinidia chinensis i... -

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Basic information

Entry
Database: PDB / ID: 3zok
TitleStructure of 3-Dehydroquinate Synthase from Actinidia chinensis in complex with NAD
Components3-DEHYDROQUINATE SYNTHASE
KeywordsLYASE / SHIKIMATE PATHWAY
Function / homology
Function and homology information


chorismate biosynthetic process => GO:0009423 / 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast / NAD binding / identical protein binding / metal ion binding
Similarity search - Function
3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLYCINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / 3-dehydroquinate synthase, chloroplastic
Similarity search - Component
Biological speciesACTINIDIA CHINENSIS (golden kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMittelstaedt, G. / Negron, L. / Schofield, L.R. / Marsh, K. / Parker, E.J.
CitationJournal: Arch. Biochem. Biophys. / Year: 2013
Title: Biochemical and structural characterisation of dehydroquinate synthase from the New Zealand kiwifruit Actinidia chinensis.
Authors: Mittelstadt, G. / Negron, L. / Schofield, L.R. / Marsh, K. / Parker, E.J.
History
DepositionFeb 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: 3-DEHYDROQUINATE SYNTHASE
B: 3-DEHYDROQUINATE SYNTHASE
C: 3-DEHYDROQUINATE SYNTHASE
D: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,22535
Polymers164,5774
Non-polymers5,64831
Water3,261181
1
A: 3-DEHYDROQUINATE SYNTHASE
B: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,20717
Polymers82,2882
Non-polymers2,91915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-78 kcal/mol
Surface area23930 Å2
MethodPISA
2
C: 3-DEHYDROQUINATE SYNTHASE
D: 3-DEHYDROQUINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,01818
Polymers82,2882
Non-polymers2,72916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-70 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.060, 150.970, 84.750
Angle α, β, γ (deg.)90.00, 101.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-DEHYDROQUINATE SYNTHASE /


Mass: 41144.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACTINIDIA CHINENSIS (golden kiwifruit) / Plasmid: PET200/ACHDHQS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: U3KRF2*PLUS, 3-dehydroquinate synthase

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Non-polymers , 8 types, 212 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNONAETHYLENE GLYCOL (2PE): 2PE MONOMER WAS ADDED BUT SHORTENED BY ONE ETHYLENE GLYCOL UNIT, THE ...NONAETHYLENE GLYCOL (2PE): 2PE MONOMER WAS ADDED BUT SHORTENED BY ONE ETHYLENE GLYCOL UNIT, THE MONOMER CODE FOR OCTAETHYLENE GLYCOL COULD NOT BE FOUND

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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: 2.22 Å3/Da / Density % sol: 44.66 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M SPG BUFFER (PH 7.0), 25% PEG 1500, 0.25 MM COCL2, 0.0003 MM NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97948
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.4→50.32 Å / Num. obs: 55631 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NR5

1nr5


Resolution: 2.4→45.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.82 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25251 2822 5.1 %RANDOM
Rwork0.18329 ---
obs0.18676 52771 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.021 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20.7 Å2
2---2.47 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11038 0 354 181 11573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211099
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.99915729
X-RAY DIFFRACTIONr_angle_other_deg0.808325483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25151456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5524.245457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51151877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7041564
X-RAY DIFFRACTIONr_chiral_restr0.0740.21807
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022518
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 183 -
Rwork0.214 3902 -
obs--99.61 %

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