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- PDB-2ohh: Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron fla... -

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Basic information

Entry
Database: PDB / ID: 2ohh
TitleCrystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, active oxidized state
ComponentsType A flavoprotein fprA
KeywordsOXIDOREDUCTASE / beta-lactamase like domain / flavodoxine like domain
Function / homology
Function and homology information


coenzyme F420H2 oxidase / FMN binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily ...Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / Coenzyme F420H(2) oxidase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeedorf, H. / Warkentin, E. / Ermler, U.
CitationJournal: Febs J. / Year: 2007
Title: Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.
Authors: Seedorf, H. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Warkentin, E. / Ermler, U.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type A flavoprotein fprA
B: Type A flavoprotein fprA
D: Type A flavoprotein fprA
E: Type A flavoprotein fprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,39117
Polymers181,0224
Non-polymers2,36813
Water16,664925
1
A: Type A flavoprotein fprA
B: Type A flavoprotein fprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6478
Polymers90,5112
Non-polymers1,1366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-98 kcal/mol
Surface area28720 Å2
MethodPISA
2
D: Type A flavoprotein fprA
E: Type A flavoprotein fprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7439
Polymers90,5112
Non-polymers1,2327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-122 kcal/mol
Surface area28270 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18520 Å2
ΔGint-242 kcal/mol
Surface area51390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.740, 120.860, 92.690
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type A flavoprotein fprA / FMN-protein fprA / Flavoprotein A


Mass: 45255.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: DSMZ2133 / Gene: fprA, fpaA / Production host: Escherichia coli (E. coli) / References: UniProt: Q50497, Oxidoreductases
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.001M DDT, 0.2M ammonium sulfate, 0.1M MES/KOH, 30% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2005 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 156544 / Num. obs: 156544 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 7.8 / Net I/σ(I): 9.9
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rugredoxin:NO/NO2 oxidoreductase from Moorella thermoacetica

Resolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.291 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21843 8277 5 %RANDOM
Rwork0.18424 ---
all0.18595 156544 --
obs0.18595 156544 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20.56 Å2
2--1.91 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12648 0 137 925 13710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213383
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.97918182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.96251628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1723.912616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.349152287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71585
X-RAY DIFFRACTIONr_chiral_restr0.1210.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210103
X-RAY DIFFRACTIONr_nbd_refined0.2280.28735
X-RAY DIFFRACTIONr_nbtor_refined0.3280.29460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.21579
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.235
X-RAY DIFFRACTIONr_mcbond_it1.1571.58243
X-RAY DIFFRACTIONr_mcangle_it1.54213053
X-RAY DIFFRACTIONr_scbond_it2.72435930
X-RAY DIFFRACTIONr_scangle_it3.9574.55129
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 613 -
Rwork0.252 11242 -
obs--98.84 %
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)
10.8353-0.0579-0.060.575-0.19530.7347-0.0771-0.0807-0.13280.11220.0551-0.0937-0.029-0.00630.0220.00130.0438-0.0476-0.096-0.01160.074441.72749.06349.035
21.31920.17170.24590.3659-0.15350.7029-0.11360.19960.053-0.02120.1045-0.03270.0125-0.00350.00910.0023-0.036-0.0141-0.0687-0.00220.034331.29369.38420.671
32.12440.6749-0.61841.0655-0.39291.6571-0.30010.90140.2322-0.13490.40390.14930.003-0.4963-0.1038-0.0916-0.1323-0.07360.34390.1651-0.0693-0.85865.6266.896
41.34470.13960.24180.4321-0.41851.3737-0.0656-0.0280.09170.07240.09910.0306-0.1206-0.0574-0.03350.01160.049-0.0047-0.10050.0090.025110.45463.53841.488
50.5489-0.02130.00460.5067-0.19321.5065-0.08640.2019-0.0782-0.0940.0752-0.1544-0.05540.14560.0112-0.0617-0.09230.07680.0709-0.14550.001239.90747.106-0.596
60.80980.3268-0.4160.502-0.44081.2692-0.06340.12-0.2775-0.01010.065-0.11810.080.0105-0.0017-0.06510.00130.0182-0.0701-0.10880.149230.06327.73628.811
70.57570.14290.12830.5299-0.21120.7306-0.02520.0214-0.05350.06160.0812-0.0221-0.027-0.0583-0.056-0.01970.01990.0021-0.08690.00180.0538-0.44234.08245.643
81.36180.2165-0.58280.4093-0.4441.2748-0.06990.2626-0.1493-0.03780.0848-0.03010.029-0.0416-0.0149-0.0597-0.07980.01550.0512-0.1095-0.02278.2235.16810.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2502 - 250
2X-RAY DIFFRACTION2AA251 - 403251 - 403
3X-RAY DIFFRACTION3BB2 - 2502 - 250
4X-RAY DIFFRACTION4BB251 - 403251 - 403
5X-RAY DIFFRACTION5DC2 - 2502 - 250
6X-RAY DIFFRACTION6DC251 - 403251 - 403
7X-RAY DIFFRACTION7ED2 - 2502 - 250
8X-RAY DIFFRACTION8ED251 - 403251 - 403

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