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- PDB-6zlf: Aerobic crystal structure of F420H2-Oxidase from Methanothermococ... -

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Basic information

Entry
Database: PDB / ID: 6zlf
TitleAerobic crystal structure of F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution under 125 bars of krypton
ComponentsCoenzyme F420H2 oxidase (FprA)
KeywordsOXIDOREDUCTASE / Krypton derivatization / oxidase / O2
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
MU-OXO-DIIRON / FLAVIN MONONUCLEOTIDE / HEXANE-1,6-DIOL / KRYPTON / F420H2 oxidase (FprA)
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEngilberge, S. / Wagner, T. / Carpentier, P. / Girard, E. / Shima, S.
Funding support France, Germany, 2items
OrganizationGrant numberCountry
French National Research Agency13-BS07-0007-01 France
Max Planck SocietyMax Planck Gesellschaft 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)
F: Coenzyme F420H2 oxidase (FprA)
G: Coenzyme F420H2 oxidase (FprA)
H: Coenzyme F420H2 oxidase (FprA)
I: Coenzyme F420H2 oxidase (FprA)
J: Coenzyme F420H2 oxidase (FprA)
K: Coenzyme F420H2 oxidase (FprA)
L: Coenzyme F420H2 oxidase (FprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,516102
Polymers369,9388
Non-polymers11,57894
Water40,0292222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54300 Å2
ΔGint-352 kcal/mol
Surface area104540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.025, 162.553, 134.376
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 8 molecules AFGHIJKL

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


Mass: 46242.230 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSW8

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Non-polymers , 6 types, 2316 molecules

#2: Chemical...
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Fe2O
#4: Chemical...
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Kr
#5: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2222 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl (pH 8.5) containing 100 mM MgCl2 and 3.3 to 3.7 M hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→48.4 Å / Num. obs: 294021 / % possible obs: 99.28 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.035 / Net I/σ(I): 12.84
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 29192 / CC1/2: 0.465 / Rpim(I) all: 0.6

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Processing

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

6frm


Resolution: 1.8→48.4 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 -5 %
Rwork0.1821 --
obs-293968 99.28 %
Displacement parametersBiso mean: 38.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25883 0 504 2222 28609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012327194
X-RAY DIFFRACTIONf_angle_d1.223936709
X-RAY DIFFRACTIONf_chiral_restr0.14143965
X-RAY DIFFRACTIONf_plane_restr0.01324591
X-RAY DIFFRACTIONf_dihedral_angle_d20.676210095

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