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- PDB-6c85: Crystal structure of aspartate semialdehyde dehydrogenase from Bl... -

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Basic information

Entry
Database: PDB / ID: 6c85
TitleCrystal structure of aspartate semialdehyde dehydrogenase from Blastomyces dermatitidis with p-benzoquinone
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossman fold / Antifungal inhibitor complex
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 ...Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-benzoquinone / aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesBlastomyces gilchristii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDahal, G.P. / Viola, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077720 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2018
Title: Structural insights into inhibitor binding to a fungal ortholog of aspartate semialdehyde dehydrogenase.
Authors: Dahal, G.P. / Viola, R.E.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5224
Polymers80,3062
Non-polymers2162
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-7 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.351, 107.351, 223.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase


Mass: 40152.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces gilchristii (fungus) / Strain: SLH14081 / Gene: BDCG_01946 / Plasmid: pET-28a(+) / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: C5GC63
#2: Chemical ChemComp-PLQ / 1,4-benzoquinone / cyclohexa-2,5-diene-1,4-dione / QUINONE RING OF THE PLASTOQUINONE 9


Mass: 108.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: long rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium Citrate Tribasic pH 7.0, 18 % w/v PEG 3350
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→85.8 Å / Num. obs: 59089 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 52.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.7
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.96 / Num. unique obs: 4511 / CC1/2: 0.953 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hsk

3hsk


Resolution: 2.4→71.417 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2884 4.89 %RANDOM
Rwork0.1998 ---
obs0.2019 58928 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.8 Å2 / Biso mean: 64.6548 Å2 / Biso min: 34.16 Å2
Refinement stepCycle: final / Resolution: 2.4→71.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 16 102 5414
Biso mean--74.36 55.26 -
Num. residues----708

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