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- PDB-1m1y: Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein -

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Basic information

Entry
Database: PDB / ID: 1m1y
TitleChemical Crosslink of Nitrogenase MoFe Protein and Fe Protein
Components
  • (Nitrogenase molybdenum-iron protein ...) x 2
  • nitrogenase IRON protein 1
KeywordsOXIDOREDUCTASE / nitrogenase / nitrogen fixation / chemical crosslink / protein interaction
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 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 iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / Nitrogenase molybdenum-iron protein beta chain, N-terminal ...Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE-MO-S CLUSTER / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / IRON/SULFUR CLUSTER / Nitrogenase iron protein 1 / 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: 3.2 Å
AuthorsSchmid, B. / Einsle, O. / Chiu, H.J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C.
CitationJournal: Biochemistry / Year: 2002
Title: Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4- Stabilized Structure
Authors: Schmid, B. / Einsle, O. / Chiu, H.J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C.
History
DepositionJun 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_biol / struct_conn / struct_site
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 / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
E: nitrogenase IRON protein 1
F: nitrogenase IRON protein 1
G: nitrogenase IRON protein 1
H: nitrogenase IRON protein 1
I: Nitrogenase molybdenum-iron protein alpha chain
J: Nitrogenase molybdenum-iron protein beta chain
K: Nitrogenase molybdenum-iron protein alpha chain
L: Nitrogenase molybdenum-iron protein beta chain
M: nitrogenase IRON protein 1
N: nitrogenase IRON protein 1
O: nitrogenase IRON protein 1
P: nitrogenase IRON protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,06136
Polymers709,88216
Non-polymers8,17820
Water00
1
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
E: nitrogenase IRON protein 1
F: nitrogenase IRON protein 1
G: nitrogenase IRON protein 1
H: nitrogenase IRON protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,03018
Polymers354,9418
Non-polymers4,08910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Nitrogenase molybdenum-iron protein alpha chain
J: Nitrogenase molybdenum-iron protein beta chain
K: Nitrogenase molybdenum-iron protein alpha chain
L: Nitrogenase molybdenum-iron protein beta chain
M: nitrogenase IRON protein 1
N: nitrogenase IRON protein 1
O: nitrogenase IRON protein 1
P: nitrogenase IRON protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,03018
Polymers354,9418
Non-polymers4,08910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.267, 214.937, 320.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a 2-alpha - 2-beta - heterotetramer crosslinked to two Fe protein dimers, i.e. half the content of the asymmetric unit.

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Components

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Nitrogenase molybdenum-iron protein ... , 2 types, 8 molecules ACIKBDJL

#1: Protein
Nitrogenase molybdenum-iron protein alpha chain / NIFD / Nitrogenase MoFe protein alpha subunit / nitrogenase component I / dinitrogenase


Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein
Nitrogenase molybdenum-iron protein beta chain / NIFK / Nitrogenase MoFe protein beta subunit / nitrogenase component I / dinitrogenase


Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Protein , 1 types, 8 molecules EFGHMNOP

#3: Protein
nitrogenase IRON protein 1 / NIFH / nitrogenase Fe protein alpha chain / Nitrogenase component II / Nitrogenase Fe protein 1 / ...NIFH / nitrogenase Fe protein alpha chain / Nitrogenase component II / Nitrogenase Fe protein 1 / Nitrogenase reductase


Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

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Non-polymers , 5 types, 20 molecules

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


Mass: 206.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical
ChemComp-CFM / FE-MO-S CLUSTER


Mass: 775.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe7MoS9
#6: Chemical
ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S7
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: PEG 6000, NaCl, Cadaverine, Tris, pH 8.0, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
133 mg/mlprotein11
240 mMTris-HCl11pH8.0
3200 mM11NaCl
420 %(v/v)MPD11
55 mM11Na2S2O4
675 mMTris-HCl12pH8.0
7510 mMcadaverine HCl12
820.9 %(w/w)PEG600012
92 mM12Na2S2O4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 129716 / Num. obs: 105200 / % possible obs: 81.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.072 / Net I/σ(I): 13
Reflection shellResolution: 3.2→3.29 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7522 / % possible all: 70.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 225603
Reflection shell
*PLUS
% possible obs: 70.3 % / Rmerge(I) obs: 0.666

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 5293 4.1 %RANDOM
Rwork0.279 ---
all0.279 129597 --
obs0.279 105098 81.1 %-
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49244 0 220 0 49464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.44
LS refinement shellResolution: 3.2→3.22 Å
RfactorNum. reflection
Rfree0.5778 92
Rwork0.4685 -
obs-1731
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.44

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