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- PDB-6zk8: Native crystal structure of anaerobic F420H2-Oxidase from Methano... -

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Basic information

Entry
Database: PDB / ID: 6zk8
TitleNative crystal structure of anaerobic F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution
ComponentsCoenzyme F420H2 oxidase (FprA)
KeywordsOXIDOREDUCTASE / oxidase / four electron reduction / Oxygen / anaerobic
Function / homology
Function and homology information


FMN binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / F420H2 oxidase (FprA)
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsEngilberge, S. / Wagner, T. / Carpentier, P. / Girard, E. / Shima, S.
Funding support France, Germany, 2items
OrganizationGrant numberCountry
French National Research AgencyLn23 ANR- 13-BS07-0007-01 France
Max Planck SocietyMax Planck Gessellschaft Germany
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Krypton-derivatization highlights O 2 -channeling in a four-electron reducing oxidase.
Authors: Engilberge, S. / Wagner, T. / Carpentier, P. / Girard, E. / Shima, S.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme F420H2 oxidase (FprA)
O: Coenzyme F420H2 oxidase (FprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65827
Polymers92,4842
Non-polymers3,17425
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-185 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.871, 156.609, 76.065
Angle α, β, γ (deg.)90.000, 137.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-606-

PEG

21A-952-

HOH

31O-629-

HOH

41O-691-

HOH

51O-817-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 27 or resid 29...
21(chain O and (resid 1 through 27 or resid 29...
12chain D
22chain Y

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 27 or resid 29...A1 - 27
121(chain A and (resid 1 through 27 or resid 29...A29 - 30
131(chain A and (resid 1 through 27 or resid 29...A32 - 84
141(chain A and (resid 1 through 27 or resid 29...A86 - 135
151(chain A and (resid 1 through 27 or resid 29...A1 - 410
161(chain A and (resid 1 through 27 or resid 29...A1 - 410
171(chain A and (resid 1 through 27 or resid 29...A291 - 334
181(chain A and (resid 1 through 27 or resid 29...A1 - 410
191(chain A and (resid 1 through 27 or resid 29...A1 - 410
1101(chain A and (resid 1 through 27 or resid 29...A601 - 701
211(chain O and (resid 1 through 27 or resid 29...O1 - 27
221(chain O and (resid 1 through 27 or resid 29...O29 - 30
231(chain O and (resid 1 through 27 or resid 29...O32 - 84
241(chain O and (resid 1 through 27 or resid 29...O86 - 135
251(chain O and (resid 1 through 27 or resid 29...O1 - 410
261(chain O and (resid 1 through 27 or resid 29...O1 - 410
271(chain O and (resid 1 through 27 or resid 29...O291 - 334
281(chain O and (resid 1 through 27 or resid 29...O1 - 410
291(chain O and (resid 1 through 27 or resid 29...O1 - 410
2101(chain O and (resid 1 through 27 or resid 29...O501 - 601
112chain DD1
212chain YY1

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AO

#1: Protein Coenzyme F420H2 oxidase (FprA) / F420H2 oxidase (FprA)


Mass: 46242.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea)
Production host: Methanothermococcus thermolithotrophicus (archaea)
References: UniProt: A0A452CSW8

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Non-polymers , 6 types, 550 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS pH 8.5, 40% PEG 400, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.83 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.83 Å / Relative weight: 1
ReflectionResolution: 1.83→43.04 Å / Num. obs: 47259 / % possible obs: 88.8 % / Redundancy: 3.1 % / CC1/2: 0.993 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 7.7
Reflection shellResolution: 1.83→1.99 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2363 / CC1/2: 0.621 / Rpim(I) all: 0.456 / Rrim(I) all: 0.815

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FRM

6frm


Resolution: 1.83→42.89 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2467 5.22 %
Rwork0.1778 44785 -
obs0.1792 47252 67.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.43 Å2 / Biso mean: 35.9281 Å2 / Biso min: 19.11 Å2
Refinement stepCycle: final / Resolution: 1.83→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 180 535 7215
Biso mean--42.14 39.52 -
Num. residues----820
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3838X-RAY DIFFRACTION5.17TORSIONAL
12O3838X-RAY DIFFRACTION5.17TORSIONAL
21A14X-RAY DIFFRACTION5.17TORSIONAL
22O14X-RAY DIFFRACTION5.17TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.870.233260.270190962
1.87-1.90.2829200.29893173379
1.9-1.950.2864320.295165468618
1.95-1.990.3088450.27061025107028
1.99-2.040.3018760.25441361143737
2.04-2.10.2398900.24411718180847
2.1-2.160.2611140.2372156227058
2.16-2.230.24971310.22912593272470
2.23-2.310.26241660.22552884305079
2.31-2.40.22911620.22613226338887
2.4-2.510.25442100.21653457366795
2.51-2.640.25331770.20733611378898
2.64-2.810.262060.19683603380998
2.81-3.020.22322040.17963570377498
3.02-3.330.22651970.16863619381698
3.33-3.810.16191980.14473610380899
3.81-4.80.14762200.13293625384599
4.8-42.890.19032130.17613666387999

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