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- PDB-7jrf: CO-CO-BOUND NITROGENASE MOFE-PROTEIN FROM A. VINELANDII -

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Basic information

Entry
Database: PDB / ID: 7jrf
TitleCO-CO-BOUND NITROGENASE MOFE-PROTEIN FROM A. VINELANDII
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / NITROGENASE / FEMO-COFACTOR / INHIBITION
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / CARBON MONOXIDE / HYDROSULFURIC ACID / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICE / IMIDAZOLE / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsSpatzal, T. / Perez, K.A. / Buscagan, T.M. / Maggiolo, A.O. / Rees, D.C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site.
Authors: Buscagan, T.M. / Perez, K.A. / Maggiolo, A.O. / Rees, D.C. / Spatzal, T.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,92528
Polymers229,7984
Non-polymers4,12724
Water36,4982026
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34000 Å2
ΔGint-257 kcal/mol
Surface area57380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.052, 129.974, 107.223
Angle α, β, γ (deg.)90.000, 109.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase molybdenum-iron protein alpha chain / Dinitrogenase / Nitrogenase component I


Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 9 types, 2050 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#4: Chemical ChemComp-ICE / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 755.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H5N2
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#7: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2026 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Peg 4000, sodium chloride, imidazole / malate, glycerol, spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.33→39.63 Å / Num. obs: 447443 / % possible obs: 98.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.041 / Net I/σ(I): 10.4
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 65111 / CC1/2: 0.747 / Rpim(I) all: 0.434 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Q

3u7q


Resolution: 1.33→39.63 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.948 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15 22350 5 %RANDOM
Rwork0.116 ---
obs0.1177 425029 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.98 Å2 / Biso mean: 14.493 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.02 Å2
2--1.16 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 1.33→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15859 0 146 2026 18031
Biso mean--15.34 26.18 -
Num. residues----1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01316680
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715171
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.68223032
X-RAY DIFFRACTIONr_angle_other_deg1.6131.57835312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61752072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51522.625857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.343152902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3791592
X-RAY DIFFRACTIONr_chiral_restr0.1260.22117
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218640
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023562
X-RAY DIFFRACTIONr_rigid_bond_restr3.534331849
LS refinement shellResolution: 1.33→1.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 1681 -
Rwork0.235 31211 -
all-32892 -
obs--97.85 %

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