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- PDB-3p2y: Crystal structure of alanine dehydrogenase/pyridine nucleotide tr... -

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Basic information

Entry
Database: PDB / ID: 3p2y
TitleCrystal structure of alanine dehydrogenase/pyridine nucleotide transhydrogenase from Mycobacterium smegmatis
ComponentsAlanine dehydrogenase/pyridine nucleotide transhydrogenase
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / non-pathogenic species / ortholog / dehydrogenase / pyruvate
Function / homology
Function and homology information


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/pyridine nucleotide transhydrogenase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8977
Polymers39,6301
Non-polymers2676
Water6,774376
1
A: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules

A: Alanine dehydrogenase/pyridine nucleotide transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,79414
Polymers79,2602
Non-polymers53512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5190 Å2
ΔGint-57 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.760, 89.760, 179.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-361-

CA

21A-701-

HOH

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Components

#1: Protein Alanine dehydrogenase/pyridine nucleotide transhydrogenase


Mass: 39629.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0152 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QNT0, alanine dehydrogenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, ...Details: 21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 38305 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 23.517 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 42.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.82-1.8714.10.23411.1325622842230981.2
1.87-1.920.20213.739524265195.8
1.92-1.970.16918.346694265598.8
1.97-2.030.13921.846885258499
2.03-2.10.12324.845738253899.2
2.1-2.180.10228.943881242199.1
2.18-2.260.08932.942528236599.3
2.26-2.350.07438.241053227699.3
2.35-2.450.06742.239144218199.5
2.45-2.570.06145.638013211899.4
2.57-2.710.05549.535640199699.6
2.71-2.880.04855.134052191899.7
2.88-3.080.04459.631970180399.7
3.08-3.320.03867.329724169399.8
3.32-3.640.03675.126994156199.9
3.64-4.070.03479.524373143199.9
4.07-4.70.03282.621750129099.9
4.7-5.760.03180.517938110099.9
5.76-8.140.02980.714452878100
8.140.02683.8786253798.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.89 Å
Translation3 Å44.89 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L7D

1l7d


Resolution: 1.82→40.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1922 / WRfactor Rwork: 0.1606 / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8996 / SU B: 3.89 / SU ML: 0.057 / SU R Cruickshank DPI: 0.1061 / SU Rfree: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1913 5 %RANDOM
Rwork0.165 ---
obs0.1665 38192 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.05 Å2 / Biso mean: 19.0145 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 12 376 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222593
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9863570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04424.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0381517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211939
X-RAY DIFFRACTIONr_mcbond_it0.8451.51764
X-RAY DIFFRACTIONr_mcangle_it1.50922849
X-RAY DIFFRACTIONr_scbond_it2.4143829
X-RAY DIFFRACTIONr_scangle_it4.2254.5705
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 108 -
Rwork0.202 2186 -
all-2294 -
obs--80.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5457-0.0021-0.06870.4315-0.01370.50170.04330.0116-0.0873-0.04540.0106-0.0443-0.05470.0066-0.05390.0137-0.00210.00310.06680.02510.044466.153339.4878-13.0551
20.0119-0.00050.04380.1665-0.03430.40340.0073-0.00130.01290.00470.0103-0.0265-0.0506-0.0577-0.01760.0272-0.00160.01770.06670.04090.054257.003649.8573-4.3285
30.9893-0.03240.22520.2869-0.19080.3359-0.0244-0.02340.11040.05120.01430.0209-0.0578-0.05180.01010.0372-0.004-0.00150.04260.00820.041949.002747.56818.8239
40.1950.18470.12670.4772-0.24980.54730.01440.02550.0518-0.02840.01340.08320.0669-0.0043-0.02780.0087-0.0058-0.0060.08470.05170.043753.256446.1756-12.3095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 71
2X-RAY DIFFRACTION2A72 - 152
3X-RAY DIFFRACTION3A153 - 306
4X-RAY DIFFRACTION4A307 - 356

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