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- PDB-1rw4: Nitrogenase Fe protein l127 deletion variant -

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Basic information

Entry
Database: PDB / ID: 1rw4
TitleNitrogenase Fe protein l127 deletion variant
ComponentsNitrogenase iron protein 1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
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. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...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. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Nitrogenase iron protein 1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSen, S. / Igarashi, R. / Smith, A. / Johnson, M.K. / Seefeldt, L.C. / Peters, J.W.
CitationJournal: Biochemistry / Year: 2004
Title: A Conformational Mimic of the MgATP-Bound "On State" of the Nitrogenase Iron Protein.
Authors: Sen, S. / Igarashi, R. / Smith, A. / Johnson, M.K. / Seefeldt, L.C. / Peters, J.W.
History
DepositionDec 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / refine / Item: _refine.ls_percent_reflns_obs
Revision 1.4Aug 23, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The iron cluster [4Fe-4S]2+ undergoes glycerol-induced cleavage to give rise to two [2Fe- ...HETEROGEN The iron cluster [4Fe-4S]2+ undergoes glycerol-induced cleavage to give rise to two [2Fe-2S] fragments.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0183
Polymers29,5741
Non-polymers4442
Water1,78399
1
A: Nitrogenase iron protein 1
hetero molecules

A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0366
Polymers59,1482
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2780 Å2
ΔGint-73 kcal/mol
Surface area23140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.78, 133.09, 61.08
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nitrogenase iron protein 1 / Nitrogenase Fe protein 1 / Nitrogenase component II / Nitrogenase reductase


Mass: 29574.041 Da / Num. of mol.: 1 / Mutation: Leu127deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifH / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): Fe protein deletion variant / References: UniProt: P00459, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal grow
*PLUS
pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
170 mg/mlprotein11
224 %PEG400011
30.16 M11pH8.5MgCl2
520 %glycerol11
61 mMsodium dithionite11
4trishydrochloric acid11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 2.5 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.5 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 10015
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.4 % / Num. measured all: 122724 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameClassification
X-PLORrefinement
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G20

1g20


Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272223 387 random
Rwork0.220391 --
all0.222 10015 -
obs0.222 10015 -
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 10 99 2159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d2.714
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.272 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.7

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