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- PDB-2vhy: Crystal structure of apo L-alanine dehydrogenase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 2vhy
TitleCrystal structure of apo L-alanine dehydrogenase from Mycobacterium tuberculosis
ComponentsALANINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD / SECRETED
Function / homology
Function and homology information


alanine catabolic process / alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / cell wall / peptidoglycan-based cell wall / response to hypoxia / nucleotide binding / extracellular region / metal ion binding ...alanine catabolic process / alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / cell wall / peptidoglycan-based cell wall / response to hypoxia / nucleotide binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Alanine dehydrogenase / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain ...Alanine dehydrogenase / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alanine dehydrogenase / Alanine dehydrogenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAgren, D. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Three-Dimensional Structures of Apo- and Holo-L-Alanine Dehydrogenase from Mycobacterium Tuberculosis Reveal Conformational Changes Upon Coenzyme Binding.
Authors: Agren, D. / Stehr, M. / Berthold, C.L. / Kapoor, S. / Oehlmann, W. / Singh, M. / Schneider, G.
History
DepositionNov 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALANINE DEHYDROGENASE
B: ALANINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)79,1642
Polymers79,1642
Non-polymers00
Water86548
1
A: ALANINE DEHYDROGENASE
B: ALANINE DEHYDROGENASE

A: ALANINE DEHYDROGENASE
B: ALANINE DEHYDROGENASE

A: ALANINE DEHYDROGENASE
B: ALANINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)237,4926
Polymers237,4926
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area20770 Å2
ΔGint-149 kcal/mol
Surface area84810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)147.110, 147.110, 93.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.97754, 0.21005, 0.01697), (0.21014, 0.97766, 0.00363), (-0.01583, 0.00712, -0.99985)
Vector: -153.96642, 16.47914, -33.72772)

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Components

#1: Protein ALANINE DEHYDROGENASE / 40 KDA ANTIGEN / TB43


Mass: 39581.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30234, UniProt: P9WQB1*PLUS, alanine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXPRESSED WITH A C-TERMINAL 6XHIS TAG.

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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: 4.31 Å3/Da / Density % sol: 71.24 % / Description: NONE
Crystal growDetails: 0.4M AMMONIUM BICARBONATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 6, 2006 / Details: RH-COATED TOROIDAL SI MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 47413 / % possible obs: 97 % / Observed criterion σ(I): 2.9 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 79

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJC

1pjc


Resolution: 2.3→45 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING
Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES ARE FOR TWINNED DATA. RESIDUES A239-A258, A269-A294, A297-A301, B242-B255, B268- B293 AND B298-B301 ARE REMOVED FROM THE ...Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES ARE FOR TWINNED DATA. RESIDUES A239-A258, A269-A294, A297-A301, B242-B255, B268- B293 AND B298-B301 ARE REMOVED FROM THE MODEL SINCE THERE IS NO DENSITY FOR THESE RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 2332 4.5 %RANDOM BUT WITH TWIN RELATED REFLECTIONS IN SAME SET
Rwork0.2155 ---
obs0.2155 48604 93.2 %-
Solvent computationBsol: 50.2348 Å2 / ksol: 0.372117 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.972 Å2-7.212 Å20 Å2
2---0.972 Å20 Å2
3---1.944 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 0 48 4844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008164
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.39623
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.303 -4.5 %
Rwork0.309 4295 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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