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- PDB-6ug0: N2-bound Nitrogenase MoFe-protein from Azotobacter vinelandii -

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Basic information

Entry
Database: PDB / ID: 6ug0
TitleN2-bound Nitrogenase MoFe-protein from Azotobacter vinelandii
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Azotobacter vinelandii / MoFe-protein / Fe-protein / FeMo-cofactor / oxidized P-cluster
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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 Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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 / Nitrogenase molybdenum iron protein domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER, OXIDIZED / : / HYDROSULFURIC ACID / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / NITROGEN MOLECULE / Chem-ICE / Chem-ICZ / MOLYBDENUM ATOM / TRIETHYLENE GLYCOL / 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: 1.83 Å
AuthorsKang, W. / Hu, Y. / Ribbe, M.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM67626 United States
Department of Energy (DOE, United States)DE-SC0016510 United States
CitationJournal: Science / Year: 2020
Title: Structural evidence for a dynamic metallocofactor during N2reduction by Mo-nitrogenase.
Authors: Kang, W. / Lee, C.C. / Jasniewski, A.J. / Ribbe, M.W. / Hu, Y.
History
DepositionSep 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2020Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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
Revision 1.3Sep 30, 2020Group: Refinement description / Category: refine / Item: _refine.details
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)234,90236
Polymers229,7984
Non-polymers5,10432
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34840 Å2
ΔGint-258 kcal/mol
Surface area55090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.362, 156.967, 202.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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 genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: 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 genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifK / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 11 types, 809 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ICE / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 755.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CFe7MoS8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HDZ / NITROGEN MOLECULE / Nitrogen


Mass: 28.013 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2S
#7: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mo
#8: Chemical ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-ICZ / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 723.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CFe7MoS7 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 14-19 % w/v PEG smear high, 0.16M ammonium acetate, 0.1M sodium citrate (pH 5.0), 25.6 % v/v glycerol, 5mM Eu(II)-EGTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 237283 / % possible obs: 95.2 % / Redundancy: 11.5 % / Biso Wilson estimate: 31.55 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.061 / Rrim(I) all: 0.215 / Net I/σ(I): 11.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 9 % / Num. unique obs: 225235 / CC1/2: 0.352 / Rpim(I) all: 1.035 / Rrim(I) all: 3.163 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERv2.8.3phasing
PHENIXv1.16-3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U7Q

3u7q


Resolution: 1.83→39.19 Å / SU ML: 0.3038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Authors state that the electron density of metal clusters presented in validation report and wwPDB websites are calculated from general pipeline without applying specific geometry restraints ...Details: Authors state that the electron density of metal clusters presented in validation report and wwPDB websites are calculated from general pipeline without applying specific geometry restraints of the clusters. To reproduce accurate difference electron density map for the clusters, users should take the author-provided map coefficients presented in the structure factor file of the entry.
RfactorNum. reflection% reflection
Rfree0.2587 1969 0.88 %
Rwork0.2176 220670 -
obs0.218 222639 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.87 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15576 0 159 777 16512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008916132
X-RAY DIFFRACTIONf_angle_d0.992721923
X-RAY DIFFRACTIONf_chiral_restr0.0542327
X-RAY DIFFRACTIONf_plane_restr0.00662803
X-RAY DIFFRACTIONf_dihedral_angle_d3.912710367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.47221190.420713481X-RAY DIFFRACTION80.88
1.87-1.920.41971390.366315863X-RAY DIFFRACTION95.48
1.92-1.980.39151420.32615956X-RAY DIFFRACTION96.03
1.98-2.040.38121440.309515978X-RAY DIFFRACTION95.8
2.04-2.120.34891410.292915869X-RAY DIFFRACTION95.11
2.12-2.20.30581420.244715767X-RAY DIFFRACTION94.75
2.2-2.30.22561390.229115554X-RAY DIFFRACTION93
2.3-2.420.24641420.221915762X-RAY DIFFRACTION94.29
2.42-2.580.32821400.225315709X-RAY DIFFRACTION93.75
2.58-2.770.28361400.234715666X-RAY DIFFRACTION93.31
2.77-3.050.28971380.224815364X-RAY DIFFRACTION91.41
3.05-3.490.24141430.2115905X-RAY DIFFRACTION93.88
3.49-4.40.20711460.180116560X-RAY DIFFRACTION97.46
4.4-39.190.20181540.174617236X-RAY DIFFRACTION98.38
Refinement TLS params.Method: refined / Origin x: 30.9250854555 Å / Origin y: 118.258636614 Å / Origin z: 151.142986479 Å
111213212223313233
T0.270326663603 Å2-0.00125179540908 Å2-0.00661536699798 Å2-0.61562283039 Å20.298919290554 Å2--0.349317662989 Å2
L0.285708256624 °20.0376183238159 °20.0690139278175 °2-0.168224924614 °20.0280775137112 °2--1.26928753563 °2
S-0.0183768278481 Å °-0.191977593123 Å °-0.0221662138007 Å °0.0759290198957 Å °-0.0411657747129 Å °-0.0101123774713 Å °0.0211009921796 Å °-0.0615852758828 Å °0.00826352825808 Å °
Refinement TLS groupSelection details: all

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