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- PDB-3b4y: FGD1 (Rv0407) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3b4y
TitleFGD1 (Rv0407) from Mycobacterium tuberculosis
ComponentsPROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1
KeywordsOXIDOREDUCTASE / TIM-barrel / non-prolyl cis-peptide bulge / F420 binding / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (coenzyme-F420) / glucose-6-phosphate dehydrogenase (coenzyme F420) activity / Cell redox homeostasis / coenzyme F420 binding / oxidoreductase activity, acting on CH-OH group of donors / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / cell redox homeostasis / peptidoglycan-based cell wall / carbohydrate metabolic process / plasma membrane / cytosol
Similarity search - Function
F420-dependent glucose-6-phosphate dehydrogenase / F420-dependent glucose-6-phosphate dehydrogenase-related / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COENZYME F420 / CITRATE ANION / F420-dependent glucose-6-phosphate dehydrogenase / F420-dependent glucose-6-phosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBashiri, G. / Squire, C.J. / Moreland, N.M. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structures of F420-dependent glucose-6-phosphate dehydrogenase FGD1 involved in the activation of the anti-tuberculosis drug candidate PA-824 reveal the basis of coenzyme and substrate binding
Authors: Bashiri, G. / Squire, C.J. / Moreland, N.J. / Baker, E.N.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2024Group: 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1
B: PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3386
Polymers79,4122
Non-polymers1,9254
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-13 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.078, 89.907, 80.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

21B-402-

HOH

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Components

#1: Protein PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1 / Glucose-6-phosphate dehydrogenase / F420-dependent


Mass: 39706.125 Da / Num. of mol.: 2 / Mutation: L243(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37-Rv / Gene: Rv0407 / Plasmid: pYUB1049 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): mc2 4517
References: UniProt: P96253, UniProt: P9WNE1*PLUS, Oxidoreductases
#2: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2007 / Details: osmic
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25.18 Å / Num. all: 47109 / Num. obs: 47019 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 17.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.2 / Num. unique all: 13127 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an in-house apo structure (itself solved by Se-MAD)

Resolution: 1.95→24.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.78 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.189 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23434 2330 5 %RANDOM
Rwork0.19174 ---
all0.19385 44565 --
obs0.19385 44565 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--0.46 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 114 195 5449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225419
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9757376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44323.2250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30115820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4481543
X-RAY DIFFRACTIONr_chiral_restr0.1160.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024235
X-RAY DIFFRACTIONr_nbd_refined0.1990.22603
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.29
X-RAY DIFFRACTIONr_mcbond_it0.7521.53404
X-RAY DIFFRACTIONr_mcangle_it1.2125282
X-RAY DIFFRACTIONr_scbond_it2.07232322
X-RAY DIFFRACTIONr_scangle_it2.5874.52090
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 171 -
Rwork0.319 3070 -
obs--92.1 %
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)
10.8916-0.194-0.25750.67070.02840.82060.0367-0.0976-0.02980.1313-0.01680.06340.1116-0.0028-0.01990.1814-0.0291-0.0008-0.14170.0093-0.0592-8.84425.62536.252
20.60890.1147-0.14230.550.06380.56980.03030.0438-0.0214-0.1502-0.0077-0.03340.08670.0105-0.02260.21110.02110.0021-0.1468-0.0031-0.05664.18624.1543.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 334
2X-RAY DIFFRACTION1A338
3X-RAY DIFFRACTION1A337
4X-RAY DIFFRACTION2B3 - 334
5X-RAY DIFFRACTION2B338
6X-RAY DIFFRACTION2B337

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