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- PDB-2ep5: Structural study of Project ID ST1242 from Sulfolobus tokodaii strain7 -

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Basic information

Entry
Database: PDB / ID: 2ep5
TitleStructural study of Project ID ST1242 from Sulfolobus tokodaii strain7
Components350aa long hypothetical aspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / amino acid biosynthetic process / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / 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 ...Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / 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
Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural study of Project ID ST1242 from Sulfolobus tokodaii strain7
Authors: Asada, Y. / Kunishima, N.
History
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 350aa long hypothetical aspartate-semialdehyde dehydrogenase
B: 350aa long hypothetical aspartate-semialdehyde dehydrogenase
C: 350aa long hypothetical aspartate-semialdehyde dehydrogenase
D: 350aa long hypothetical aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)154,9774
Polymers154,9774
Non-polymers00
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-55 kcal/mol
Surface area50790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.157, 73.986, 91.552
Angle α, β, γ (deg.)68.102, 68.393, 86.036
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
350aa long hypothetical aspartate-semialdehyde dehydrogenase


Mass: 38744.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: strain7 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CodonPlus(DE3)-RIL
References: UniProt: Q971Y6, aspartate-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: 8w/v(%) PEG 4K, 0.1M Acet, pH 4.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 58141 / Num. obs: 58141 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 34.173 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 4.18 / % possible all: 94.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.27 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2901 -RAMDOM
Rwork0.191 ---
all0.194 58141 --
obs0.194 58141 94.3 %-
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å24.73 Å2-2.31 Å2
2--7.19 Å2-2.25 Å2
3----3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10823 0 0 677 11500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.288 348 -
Rwork0.228 --
obs--88.8 %

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