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- PDB-3vos: Crystal structure of Aspartate semialdehyde dehydrogenase Complex... -

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Basic information

Entry
Database: PDB / ID: 3vos
TitleCrystal structure of Aspartate semialdehyde dehydrogenase Complexed With glycerol and sulfate From Mycobacterium tuberculosis H37Rv
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / AMINO-ACID BIOSYNTHESIS / LYSINE BIOSYNTHESIS
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / cell wall / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / NAD binding ...aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / cell wall / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / NAD binding / NADP binding / protein dimerization activity / plasma membrane
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 / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsVyas, R. / Tewari, R. / Weiss, M.S. / Karthikeyan, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of ternary complexes of aspartate-semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv
Authors: Vyas, R. / Tewari, R. / Weiss, M.S. / Karthikeyan, S.
History
DepositionFeb 7, 2012Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 30, 2012ID: 3LLG
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,96710
Polymers38,1141
Non-polymers8539
Water6,161342
1
A: Aspartate-semialdehyde dehydrogenase
hetero molecules

A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,93320
Polymers76,2282
Non-polymers1,70518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
Buried area7200 Å2
ΔGint-33 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)267.370, 267.370, 267.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

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


Mass: 38114.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: asd, MT3811, MTV025.056c, Rv3708c / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P0A542, UniProt: P9WNX5*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 5.24 Å3/Da / Density % sol: 76.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100MM CITRIC ACID, 1.6M AMSO4, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.067 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2007 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.067 Å / Relative weight: 1
ReflectionResolution: 2.18→99 Å / Num. all: 43078 / Num. obs: 43078 / % possible obs: 99.9 % / Observed criterion σ(F): 2.18 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 14.1
Reflection shellResolution: 2.18→2.22 Å / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.953

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GYY

2gyy


Resolution: 2.18→32.42 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.014 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19444 1987 4.6 %RANDOM
Rwork0.18062 ---
obs0.18126 41079 99.87 %-
all-43078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.848 Å2
Refinement stepCycle: LAST / Resolution: 2.18→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 48 342 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192586
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9983517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00923.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.581523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211942
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 123 -
Rwork0.26 2678 -
obs--99.82 %

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