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- PDB-3tz6: Crystal structure of Aspartate semialdehyde dehydrogenase Complex... -

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Basic information

Entry
Database: PDB / ID: 3tz6
TitleCrystal structure of Aspartate semialdehyde dehydrogenase Complexed With inhibitor SMCS (CYS) And Phosphate From Mycobacterium tuberculosis H37Rv
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ASADH / ASD / ASA / DEHYDROGENASE / AMINO-ACID BIOSYNTHESIS / DIAMINOPIMELATE BIOSYNTHESIS / LYSINE BIOSYNTHESIS / SMCS
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
CYSTEINE / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionSep 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,10811
Polymers36,1341
Non-polymers97410
Water6,630368
1
A: Aspartate-semialdehyde dehydrogenase
hetero molecules

A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,21522
Polymers72,2682
Non-polymers1,94820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
Buried area7280 Å2
ΔGint-32 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.160, 266.160, 266.160
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-892-

HOH

21A-1011-

HOH

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Components

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


Mass: 36133.848 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: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: P0A542, UniProt: P9WNX5*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 5.26 Å3/Da / Density % sol: 76.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 100MM CITRIC ACID, 1.6M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 14, 2010 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 58288 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.59
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.21 / Rsym value: 0.728 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLG

3llg
PDB Unreleased entry


Resolution: 1.95→29.2 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.499 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 1.33 / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21072 2958 5.1 %RANDOM
Rwork0.19168 ---
obs0.19266 55335 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 55 368 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.0013648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62224.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50315421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5711523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 188 -
Rwork0.276 3750 -
obs--99.12 %

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