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- PDB-6frm: Crystal Structure of coenzyme F420H2 oxidase (FprA) co-crystalliz... -

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Basic information

Entry
Database: PDB / ID: 6frm
TitleCrystal Structure of coenzyme F420H2 oxidase (FprA) co-crystallized with 10 mM Tb-Xo4
ComponentsCoenzyme F420H2 oxidase (FprA)
KeywordsOXIDOREDUCTASE / Tb-Xo4 / crystallophore / FprA / nucleation / phasing / anomalous
Function / homology
Function and homology information


FMN binding / electron transfer activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Flavodoxin ...Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Flavodoxin / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tb-Xo4 / : / FLAVIN MONONUCLEOTIDE / TERBIUM(III) ION / F420H2 oxidase (FprA)
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEngilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 France
CitationJournal: Chemistry / Year: 2018
Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.
Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Structure summary / Category: entity / pdbx_seq_map_depositor_info
Item: _entity.pdbx_description / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 29, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_seq_map_depositor_info
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme F420H2 oxidase (FprA)
B: Coenzyme F420H2 oxidase (FprA)
C: Coenzyme F420H2 oxidase (FprA)
D: Coenzyme F420H2 oxidase (FprA)
E: Coenzyme F420H2 oxidase (FprA)
F: Coenzyme F420H2 oxidase (FprA)
G: Coenzyme F420H2 oxidase (FprA)
H: Coenzyme F420H2 oxidase (FprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,75253
Polymers369,9388
Non-polymers7,81445
Water28,4821581
1
A: Coenzyme F420H2 oxidase (FprA)
B: Coenzyme F420H2 oxidase (FprA)
C: Coenzyme F420H2 oxidase (FprA)
D: Coenzyme F420H2 oxidase (FprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,85826
Polymers184,9694
Non-polymers3,89022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20730 Å2
ΔGint-246 kcal/mol
Surface area54490 Å2
MethodPISA
2
E: Coenzyme F420H2 oxidase (FprA)
F: Coenzyme F420H2 oxidase (FprA)
G: Coenzyme F420H2 oxidase (FprA)
H: Coenzyme F420H2 oxidase (FprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,89427
Polymers184,9694
Non-polymers3,92523
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-260 kcal/mol
Surface area54210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.170, 147.875, 146.059
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Coenzyme F420H2 oxidase (FprA)


Mass: 46242.230 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus (archaea)
References: UniProt: A0A452CSW8*PLUS

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Non-polymers , 6 types, 1626 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#4: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Tb
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1581 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: FprA native (about 90 % pure) at 43 g/l + 10 mM Xo4, crystallized at 291 K under anaerobic condition (95% N2 / 5% H2) in Combiclover Junior plate from Jena Bioscience. The protein was ...Details: FprA native (about 90 % pure) at 43 g/l + 10 mM Xo4, crystallized at 291 K under anaerobic condition (95% N2 / 5% H2) in Combiclover Junior plate from Jena Bioscience. The protein was crystallized by mixing 1 ul protein of this mix with 1 ul of the mother liquor containing 20% w/v PEG 8000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate and 10 % v/v 2-propanol. Prior to freezing in liquid nitrogen, the crystal was soaked for few seconds in a cryo-protected solution containing: 20% w/v PEG 8000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate, 10 % v/v 2-propanol, 25 % v/v glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.19→48.69 Å / Num. obs: 181493 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 44.22 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 9
Reflection shellResolution: 2.19→2.31 Å / Rpim(I) all: 0.534

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OHH

2ohh


Resolution: 2.2→48.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.209 8913 4.99 %RANDOM
Rwork0.177 ---
obs0.178 178580 98.8 %-
Displacement parametersBiso mean: 52.27 Å2
Baniso -1Baniso -2Baniso -3
1--3.0461 Å20 Å22.1485 Å2
2--0.7493 Å20 Å2
3---2.2968 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.2→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25515 0 343 1609 27467
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126503HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1635806HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9227SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes628HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3966HARMONIC12
X-RAY DIFFRACTIONt_it26503HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.82
X-RAY DIFFRACTIONt_other_torsion18.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact31186SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 591 4.96 %
Rwork0.3666 11315 -
all0.3679 11906 -
obs--89.22 %
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)
10.4483-0.14010.19791.2657-0.54790.92080.0644-0.0359-0.01390.1368-0.0645-0.1732-0.05850.2480.00010.0686-0.0612-0.00340.2581-0.0156-0.1948-46.08125.585134.4243
20.44010.4207-0.07951.0624-0.33410.95640.03640.1424-0.0382-0.0777-0.0261-0.11460.14530.244-0.01030.03150.04870.04090.3047-0.0443-0.192-48.81346.33652.3659
30.57290.1226-0.23640.548-0.43771.62-0.00030.1685-0.0623-0.02250.05390.11790.2748-0.2489-0.05350.1113-0.08540.0220.2236-0.0359-0.1841-83.9205-4.803918.1839
40.66120.06670.20.7464-0.1581.27710.01670.04170.22130.0748-0.03850.1596-0.3158-0.13930.02180.12730.01710.07180.1621-0.007-0.1383-78.906826.788324.6494
50.4160.38520.10611.11160.36990.6112-0.03130.14910.005-0.12520.01090.12050.0276-0.08370.02030.0592-0.02860.02070.25090.0289-0.1501-102.00743.9517-70.6233
60.397-0.237-0.00831.19050.37840.6507-0.006-0.0394-0.03320.0985-0.04410.16540.151-0.11160.05010.0581-0.0520.08810.23130.0274-0.1326-104.52084.6714-38.7751
70.381-0.0831-0.14420.80840.5831.19590.00490.0033-0.13170.13510.0442-0.09310.24880.1879-0.04920.15480.0770.01850.1930.0189-0.1637-71.322-15.4728-48.187
80.33470.10490.29260.63840.42531.4285-0.04590.10040.0562-0.02910.0768-0.0866-0.08520.2184-0.03090.0361-0.02130.04780.26340.0252-0.1432-67.211616.4192-54.8176
90.09060.08280.13470.1203-0.00620.47360.0090.0360.00430.0142-0.00720.02340.06040.0734-0.00190.06250.00750.0620.16820.0055-0.1182-75.39955.4974-16.6514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }

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