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- PDB-3b4w: Crystal structure of Mycobacterium tuberculosis aldehyde dehydrog... -

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Basic information

Entry
Database: PDB / ID: 3b4w
TitleCrystal structure of Mycobacterium tuberculosis aldehyde dehydrogenase complexed with NAD+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rv0223c-NAD complex / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


NADH binding / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / AMP binding / FAD binding / ADP binding / NAD binding / ATP binding / plasma membrane
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMoon, J.H. / Lyon, A.E. / Yu, M. / Hung, L.-W. / Terwilliger, T. / Kim, C.-Y. / Integrated Center for Structure and Function Innovation (ISFI) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To Be Published
Title: X-ray crystal structure of aldehyde dehydrogenase from Mycobacterium tuberculosis complexed with NAD+.
Authors: Moon, J.H. / Lyon, A.E. / Yu, M. / Hung, L.-W. / Terwilliger, T. / Kim, C.-Y.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53211
Polymers52,1701
Non-polymers1,36210
Water7,945441
1
A: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,06422
Polymers104,3402
Non-polymers2,72420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.111, 135.111, 72.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1178-

HOH

DetailsAuthors state that the biological unit of this protein is unknown.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aldehyde dehydrogenase /


Mass: 52170.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0223c, MT0233 / Plasmid: Modified pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P96405, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 451 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 0.8 M Ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795, 0.9800, 0.9600
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.981
30.961
ReflectionResolution: 1.8→39.896 Å / Num. all: 63594 / Num. obs: 62513 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6234 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.896 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 5471 4.9 %RANDOM
Rwork0.168 ---
all0.1693 57064 --
obs0.1693 57064 --
Displacement parametersBiso mean: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.4518 Å20 Å20 Å2
2--0.4518 Å20 Å2
3----0.9035 Å2
Refine analyzeLuzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 87 441 4096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.209
X-RAY DIFFRACTIONf_dihedral_angle_d18.283
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2809 144 -
Rwork0.2394 --
obs-3050 80.39 %

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