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- PDB-5lxe: F420-dependent glucose-6-phosphate dehydrogenase from Rhodococcus... -

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Basic information

Entry
Database: PDB / ID: 5lxe
TitleF420-dependent glucose-6-phosphate dehydrogenase from Rhodococcus jostii RHA1
ComponentsF420-dependent glucose-6-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / F420 / glucose-6-phosphate dehydrogenase / TIM barrel / bacterial luciferase family
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (coenzyme-F420) / glucose-6-phosphate dehydrogenase (coenzyme F420) activity / coenzyme F420 binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / carbohydrate metabolic process
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
F420-dependent glucose-6-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsNguyen, Q.-T. / Trinco, G. / Binda, C. / Mattevi, A. / Fraaije, M.W.
Funding support Italy, Netherlands, 2items
OrganizationGrant numberCountry
The European Community Seventh Framework ProgrammeFP7 (2007--2013) under BioStruct-X (Grants 7551 and 10205) Italy
University of GroningenUbbo Emmius scholarship Netherlands
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Discovery and characterization of an F420-dependent glucose-6-phosphate dehydrogenase (Rh-FGD1) from Rhodococcus jostii RHA1.
Authors: Nguyen, Q.-T. / Trinco, G. / Binda, C. / Mattevi, A. / Fraaije, M.W.
History
DepositionSep 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F420-dependent glucose-6-phosphate dehydrogenase 1
B: F420-dependent glucose-6-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3546
Polymers73,9782
Non-polymers3764
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.540, 88.120, 88.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHEAA1 - 401 - 40
21METMETPHEPHEBB1 - 401 - 40
12ALAALALEULEUAA50 - 33450 - 334
22ALAALALEULEUBB50 - 33450 - 334

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.960155, 0.003353, 0.279448), (0.002749, -0.999766, 0.02144), (0.279455, 0.021354, 0.959921)-48.62352, -30.91676, 7.28584

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Components

#1: Protein F420-dependent glucose-6-phosphate dehydrogenase 1 / G6PD 1


Mass: 36988.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The gap in the sequence alignment is due to the disorder in the electron density map.
Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria)
Gene: fgd1, RHA1_ro11062 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0RVH7, glucose-6-phosphate dehydrogenase (coenzyme-F420)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, sodium acetate pH 4.6, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.71, 2.25
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.711
22.251
ReflectionResolution: 1.47→88.78 Å / Num. obs: 106774 / % possible obs: 98.7 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.9
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B4Y

3b4y


Resolution: 1.47→62.54 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.315 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 5293 5 %RANDOM
Rwork0.15632 ---
obs0.15778 101407 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20 Å2
2---1.51 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.47→62.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 22 571 5475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195080
X-RAY DIFFRACTIONr_bond_other_d0.0020.024787
X-RAY DIFFRACTIONr_angle_refined_deg2.021.966889
X-RAY DIFFRACTIONr_angle_other_deg1.074311002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36922.931232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76215812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281543
X-RAY DIFFRACTIONr_chiral_restr0.1290.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215788
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021191
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1352.172541
X-RAY DIFFRACTIONr_mcbond_other2.1352.1692540
X-RAY DIFFRACTIONr_mcangle_it2.9493.2453178
X-RAY DIFFRACTIONr_mcangle_other2.953.2463179
X-RAY DIFFRACTIONr_scbond_it3.522.6022539
X-RAY DIFFRACTIONr_scbond_other3.5162.6032539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3373.7413710
X-RAY DIFFRACTIONr_long_range_B_refined6.7427.5395864
X-RAY DIFFRACTIONr_long_range_B_other6.7427.5455865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4471 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.620.5
Bmedium thermal3.672
LS refinement shellResolution: 1.474→1.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 358 -
Rwork0.271 7355 -
obs--97.2 %

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