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- PDB-4lmp: Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structur... -

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Basic information

Entry
Database: PDB / ID: 4lmp
TitleMycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-methyl adenosine
ComponentsAlanine dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Susceptibility to Known Mtb Inhibitors / MTBI / Rossmann Fold / N6-methyl adenosine binding / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / N-methyladenosine / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, H.-B. / Hung, L.-W. / Goulding, C.W. / Terwilliger, T.C. / Kim, C.-Y. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Drug target analysis by dye-ligand affinity chromatography
Authors: Kim, H.-B. / Hung, L.-W. / Goulding, C.W. / Terwilliger, T.C. / Kim, C.-Y.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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

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Assembly

Deposited unit
A: Alanine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6919
Polymers38,7531
Non-polymers9388
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alanine dehydrogenase
hetero molecules

A: Alanine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,38218
Polymers77,5062
Non-polymers1,87616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area7250 Å2
ΔGint-115 kcal/mol
Surface area26260 Å2
MethodPISA
3
A: Alanine dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)238,14654
Polymers232,5196
Non-polymers5,62748
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area31060 Å2
ΔGint-364 kcal/mol
Surface area69480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.730, 89.730, 290.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein Alanine dehydrogenase /


Mass: 38753.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ald, RVBD_2780 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YEC9, alanine dehydrogenase
#2: Chemical ChemComp-6MD / N-methyladenosine / N6-Methyladenosine


Mass: 281.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O4
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2M ammonium sulfate, 5% 2-propanol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010 / Details: Si111
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 33325 / Num. obs: 33325 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.84
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.234 / Num. unique all: 1602 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VHY

2vhy


Resolution: 1.95→48.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1933 6 %RANDOM
Rwork0.183 ---
all0.1857 32213 --
obs0.1857 32213 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 59 211 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082837
X-RAY DIFFRACTIONf_angle_d1.1363867
X-RAY DIFFRACTIONf_dihedral_angle_d13.4921002
X-RAY DIFFRACTIONf_chiral_restr0.075454
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99870.28591240.24371948X-RAY DIFFRACTION88
1.9987-2.05280.28971300.21691991X-RAY DIFFRACTION92
2.0528-2.11320.25751340.20512077X-RAY DIFFRACTION94
2.1132-2.18140.26021320.20052108X-RAY DIFFRACTION95
2.1814-2.25930.23131340.18862120X-RAY DIFFRACTION96
2.2593-2.34980.25111370.18682127X-RAY DIFFRACTION97
2.3498-2.45670.23461370.18372151X-RAY DIFFRACTION97
2.4567-2.58620.23481390.18832188X-RAY DIFFRACTION97
2.5862-2.74830.20891380.19562189X-RAY DIFFRACTION98
2.7483-2.96040.25161430.19022215X-RAY DIFFRACTION99
2.9604-3.25830.24481410.19772222X-RAY DIFFRACTION100
3.2583-3.72960.2131460.172274X-RAY DIFFRACTION100
3.7296-4.69830.18141450.15042274X-RAY DIFFRACTION100
4.6983-48.41510.22711530.18032396X-RAY DIFFRACTION100

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