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- PDB-2yv3: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Th... -

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Basic information

Entry
Database: PDB / ID: 2yv3
TitleCrystal Structure of Aspartate Semialdehyde Dehydrogenase from Thermus thermophilus HB8
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ASPARTATE PATHWAY / 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 / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / isoleucine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / 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 ...Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKagawa, W. / Fujikawa, N. / Kurumizaka, H. / Bessho, Y. / Ellis, M.J. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Thermus thermophilus HB8
Authors: Kagawa, W. / Fujikawa, N. / Kurumizaka, H. / Bessho, Y. / Ellis, M.J. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S. / Kuramitsu, S. / Yokoyama, S.
History
DepositionApr 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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


Theoretical massNumber of molelcules
Total (without water)72,2492
Polymers72,2492
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-30 kcal/mol
Surface area25270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.167, 125.167, 116.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase /


Mass: 36124.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q5SKU8, aspartate-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl (pH 8.2), 0.2M MgCl2, 30% PEG 4000, 3% ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9000, 0.9793
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 22, 2006
RadiationMonochromator: Si Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.91
30.97931
ReflectionResolution: 2.7→50 Å / Num. all: 29713 / Num. obs: 29493 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2832 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GZ3

2gz3


Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.368 2923 -random
Rwork0.303 ---
all0.368 29301 --
obs0.303 26378 99.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 0 45 5107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00954
X-RAY DIFFRACTIONc_angle_d1.75
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.19
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.7-2.80.4143010.305X-RAY DIFFRACTION258010
2.8-2.910.4012950.283X-RAY DIFFRACTION261710
2.91-3.040.4312960.32X-RAY DIFFRACTION259510
3.04-3.20.4043110.308X-RAY DIFFRACTION258610
3.2-3.40.3742900.309X-RAY DIFFRACTION263510
3.4-3.660.3662720.292X-RAY DIFFRACTION264610
3.66-4.030.3422870.294X-RAY DIFFRACTION264910
4.03-4.620.3272670.277X-RAY DIFFRACTION267610
4.62-5.810.3542890.302X-RAY DIFFRACTION265910
5.81-500.3713150.344X-RAY DIFFRACTION273510

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