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- PDB-7bi7: An Unexpected P-Cluster like Intermediate En Route to the Nitroge... -

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Basic information

Entry
Database: PDB / ID: 7bi7
TitleAn Unexpected P-Cluster like Intermediate En Route to the Nitrogenase FeMo-co
ComponentsFeMo cofactor biosynthesis protein NifB
KeywordsMETAL BINDING PROTEIN / NITROGENASE / RADICAL SAM ENZYME / IRON-MOLYBDENUM COFACTOR BIOSYNTHESIS
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / HYDROSULFURIC ACID / MALONATE ION / NITRATE ION / IRON/SULFUR CLUSTER / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifB
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJenner, L.P. / Cherrier, M.V. / Amara, P. / Rubio, L.M. / Nicolet, Y.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
CitationJournal: Chem Sci / Year: 2021
Title: An unexpected P-cluster like intermediate en route to the nitrogenase FeMo-co.
Authors: Jenner, L.P. / Cherrier, M.V. / Amara, P. / Rubio, L.M. / Nicolet, Y.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 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: FeMo cofactor biosynthesis protein NifB
B: FeMo cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,29110
Polymers65,0132
Non-polymers2,2788
Water19811
1
A: FeMo cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6265
Polymers32,5071
Non-polymers1,1194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FeMo cofactor biosynthesis protein NifB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6665
Polymers32,5071
Non-polymers1,1594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.870, 77.640, 90.800
Angle α, β, γ (deg.)90.000, 128.850, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FeMo cofactor biosynthesis protein NifB / Nitrogenase cofactor maturase NifB / Radical SAM assemblase NifB / nitrogenase iron-molybdenum ...Nitrogenase cofactor maturase NifB / Radical SAM assemblase NifB / nitrogenase iron-molybdenum cofactor biosynthesis protein


Mass: 32506.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_1871 / Production host: Escherichia coli (E. coli) / References: UniProt: O27899

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Non-polymers , 6 types, 19 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M SODIUM MALONATE (PH7), PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.71915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2019
RadiationMonochromator: WATER-COOLED FLAT DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71915 Å / Relative weight: 1
ReflectionResolution: 3→70.71 Å / Num. obs: 12056 / % possible obs: 90.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 87.35 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.085 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.9 % / Num. unique obs: 1215 / CC1/2: 0.581 / Rpim(I) all: 0.704 / % possible all: 63.6

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.3 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y1X

6y1x


Resolution: 3→60.84 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.419
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1207 10.03 %RANDOM
Rwork0.2019 ---
obs0.2057 12030 90.2 %-
Displacement parametersBiso max: 152.57 Å2 / Biso mean: 77.22 Å2 / Biso min: 27.59 Å2
Baniso -1Baniso -2Baniso -3
1-25.6676 Å20 Å21.6601 Å2
2---6.8925 Å20 Å2
3----18.7751 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 3→60.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 59 11 4114
Biso mean--94.81 45.39 -
Num. residues----550
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1423SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes712HARMONIC5
X-RAY DIFFRACTIONt_it4218HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion590SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance22HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3335SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4218HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5814HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion21.91
LS refinement shellResolution: 3→3.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2502 23 9.54 %
Rwork0.2422 218 -
all0.2429 241 -
obs--56.07 %
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)
12.3948-1.58790.07914.67140.23641.7628-0.1070.2297-0.144-0.19480.22160.1292-0.18340.2981-0.1145-0.1057-0.12050.11650.1326-0.0243-0.2812-11.095535.047118.8043
22.8433-0.0468-0.62111.61480.33461.9562-0.1231-0.33120.20970.07920.01110.04290.16130.23870.112-0.09780.06040.01290.09330.005-0.254-12.796326.863153.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A7 - 285
2X-RAY DIFFRACTION2{ B|* }B7 - 277

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