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- PDB-2voe: Crystal structure of Rv2780 from M. tuberculosis H37Rv -

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Basic information

Entry
Database: PDB / ID: 2voe
TitleCrystal structure of Rv2780 from M. tuberculosis H37Rv
ComponentsALANINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SECRETED / NAD / PYRUVATE
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/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / 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/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / 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 / OTHER / Resolution: 2.6 Å
AuthorsTripathi, S.M. / Ramachandran, R.
CitationJournal: Proteins / Year: 2008
Title: Crystal Structures of the Mycobacterium Tuberculosis Secretory Antigen Alanine Dehydrogenase (Rv2780) in Apo and Ternary Complex Forms Captures "Open" and "Closed" Enzyme Conformations.
Authors: Tripathi, S.M. / Ramachandran, R.
History
DepositionFeb 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALANINE DEHYDROGENASE
B: ALANINE DEHYDROGENASE
C: ALANINE DEHYDROGENASE
D: ALANINE DEHYDROGENASE
E: ALANINE DEHYDROGENASE
F: ALANINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)232,5196
Polymers232,5196
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21180 Å2
ΔGint-110.5 kcal/mol
Surface area74000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.891, 127.078, 135.954
Angle α, β, γ (deg.)90.00, 115.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 371
2112B1 - 371
3112C1 - 371
4112D1 - 371
5112E1 - 371
6112F1 - 371

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Components

#1: Protein
ALANINE DEHYDROGENASE / / 40 KDA ANTIGEN / TB43 / RV2780


Mass: 38753.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30234, UniProt: P9WQB1*PLUS, alanine dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: VARIMAX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 46867 / % possible obs: 97.6 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→123.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 10.695 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.666 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 4005 5 %RANDOM
Rwork0.19561 ---
obs0.19837 75667 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-0.91 Å2
2--0.48 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→123.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16162 0 0 224 16386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02216453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.96522428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49752220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05223.682611
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.534152483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.87715103
X-RAY DIFFRACTIONr_chiral_restr0.1350.22664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212423
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.27523
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.211176
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3810.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.511183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.469217489
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0835773
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4674.54939
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1460tight positional0.060.05
2B1460tight positional0.060.05
3C1460tight positional0.070.05
4D1460tight positional0.070.05
5E1460tight positional0.090.05
6F1460tight positional0.060.05
1A1191medium positional0.430.5
2B1191medium positional0.40.5
3C1191medium positional0.620.5
4D1191medium positional0.450.5
5E1191medium positional0.480.5
6F1191medium positional0.460.5
1A1460tight thermal0.130.5
2B1460tight thermal0.150.5
3C1460tight thermal0.180.5
4D1460tight thermal0.140.5
5E1460tight thermal0.150.5
6F1460tight thermal0.120.5
1A1191medium thermal0.872
2B1191medium thermal0.932
3C1191medium thermal1.072
4D1191medium thermal0.822
5E1191medium thermal0.962
6F1191medium thermal0.812
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 214
Rwork0.293 4683

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