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- PDB-2qz9: crystal structure of aspartate semialdehyde dehydrogenase II from... -

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Basic information

Entry
Database: PDB / ID: 2qz9
Titlecrystal structure of aspartate semialdehyde dehydrogenase II from vibrio cholerae
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aspartate semialdehyde dehydrogenase / conformational changes / half-of-sites-reactivity / protein evolution / sequence homology / subunit communication / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / NADP
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine 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, conserved site / Aspartate-semialdehyde dehydrogenase / 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 ...Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / 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
Aspartate-semialdehyde dehydrogenase 2
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsViola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae.
Authors: Viola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
C: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)111,8343
Polymers111,8343
Non-polymers00
Water7,512417
1
A: Aspartate-semialdehyde dehydrogenase
C: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5562
Polymers74,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-26.9 kcal/mol
Surface area24640 Å2
MethodPISA
2
B: Aspartate-semialdehyde dehydrogenase

B: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5562
Polymers74,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4620 Å2
ΔGint-21.8 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.327, 85.655, 116.101
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-395-

HOH

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase / ASA dehydrogenase / ASADH


Mass: 37277.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: E1 Tor N16961 / Gene: asd / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P23247, aspartate-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% PEG8000, 0.2M ammonium sulfate, 5mM DTT, 0.1M sodium citrate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 57268 / Num. obs: 54355 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 23
Reflection shellHighest resolution: 2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / Num. unique all: 57268 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PEB entry 1YS4

1ys4


Resolution: 2.2→37.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.287 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 2914 5.1 %RANDOM
Rwork0.19827 ---
obs0.20091 54355 99.27 %-
all-57268 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7852 0 0 417 8269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228014
X-RAY DIFFRACTIONr_angle_refined_deg1.21.93510899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90351004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28825.012403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.644151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7561545
X-RAY DIFFRACTIONr_chiral_restr0.0840.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026216
X-RAY DIFFRACTIONr_nbd_refined0.1990.23662
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2454
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.218
X-RAY DIFFRACTIONr_mcbond_it0.6661.55157
X-RAY DIFFRACTIONr_mcangle_it1.18628096
X-RAY DIFFRACTIONr_scbond_it1.47733237
X-RAY DIFFRACTIONr_scangle_it2.2954.52803
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 206 -
Rwork0.245 3779 -
obs--94.34 %

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