[English] 日本語
Yorodumi
- PDB-3b4y: FGD1 (Rv0407) from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
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 / coenzyme F420 binding / Cell redox homeostasis / oxidoreductase activity, acting on CH-OH group of donors / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / peptidoglycan-based cell wall / cell redox homeostasis / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Coenzyme F420


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more