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- PDB-29ul: Mo-Nitrogenase, MoFe protein, P3+ redox state, +150 mV -

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Basic information

Entry
Database: PDB / ID: 29ul
TitleMo-Nitrogenase, MoFe protein, P3+ redox state, +150 mV
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Mo-Nitrogenase / MoFe protein / P3+ redox state / +150 mV
Function / homology
Function and homology information


nitrogen fixation / molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / 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, OXIDIZED / ACETATE ION / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLaxmi, S. / Seefeldt, L.C. / Carr, S.B. / Vincent, K.A.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
Department of Energy (DOE, United States)DE-SC0010687 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Structural Characterization of Four Redox States of the P-cluster in Molybdenum Nitrogenase via Electrochemical Control of Crystals
Authors: Laxmi, S. / Myers, W.K. / Yang, Z.Y. / Seefeldt, L.C. / Carr, S.B. / Vincent, K.A.
History
DepositionApr 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Nitrogenase molybdenum-iron protein alpha chain
F: Nitrogenase molybdenum-iron protein beta chain
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,31914
Polymers232,7774
Non-polymers3,54210
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.846, 73.351, 211.954
Angle α, β, γ (deg.)90.000, 104.422, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 236 or resid 238 through 248 or resid 250 through 608))
d_2ens_1(chain "E" and (resid 4 through 236 or resid 238 through 248 or resid 250 through 608))
d_1ens_2(chain "B" and (resid 2 through 370 or resid 372 through 523))
d_2ens_2(chain "F" and (resid 2 through 370 or resid 372 through 523))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETTRPTRPAC4 - 23617 - 249
d_12ens_1SERSERARGARGAC238 - 248251 - 261
d_13ens_1VALVALGLUGLUAC250 - 480263 - 493
d_14ens_1HCAHCAHCAHCAAJ601
d_15ens_1ICSICSICSICSAK602
d_16ens_11CL1CL1CL1CLBM601
d_21ens_1METMETTRPTRPEA4 - 23617 - 249
d_22ens_1SERSERARGARGEA238 - 248251 - 261
d_23ens_1VALVALGLUGLUEA250 - 480263 - 493
d_24ens_1HCAHCAHCAHCAEE601
d_25ens_1ICSICSICSICSEF602
d_26ens_11CL1CL1CL1CLFH601
d_11ens_2SERSERTRPTRPBD2 - 3702 - 370
d_12ens_2ASPASPARGARGBD372 - 523372 - 523
d_21ens_2SERSERTRPTRPFB2 - 3702 - 370
d_22ens_2ASPASPARGARGFB372 - 523372 - 523

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.716690618636, -0.616460981038, 0.326083449468), (-0.615729357622, -0.778890021031, -0.119196028876), (0.327462845711, -0.115352477198, -0.937796294876)-21.6546545962, -14.4964719132, 86.0741201355
2given(0.714797648415, -0.616124160311, 0.33084035561), (-0.617337917451, -0.778184658678, -0.115423276139), (0.328569958299, -0.121736009785, -0.936601370074)-21.7363678023, -14.6087467325, 85.8440051311

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Components

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

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


Mass: 56852.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mo-Nitrogenase, MoFe protein, P3+ redox state, +150 mV
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ2102 / Gene: nifD / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ2102 / 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
Details: Mo-Nitrogenase, MoFe protein, P3+ redox state, +150 mV
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ2102 / Gene: nifK / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ2102 / References: UniProt: P07329, nitrogenase

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Non-polymers , 6 types, 26 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-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.39 % / Description: Thin, Brown Rod-shaped crystals
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 0.1 M sodium citrate pH 5.0, 0.16 M ammonium acetate, 17% (v/v) PEG Smear High, 25% (v/v) glycerol
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→52.71 Å / Num. obs: 78429 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 57.69 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.092 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.55 Å / Rmerge(I) obs: 4.606 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4454 / Rpim(I) all: 1.832 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.94 Å / SU ML: 0.4485 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.6491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2561 1634 2.11 %
Rwork0.225 75771 -
obs0.2257 77405 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15928 0 107 16 16051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005916481
X-RAY DIFFRACTIONf_angle_d0.864522364
X-RAY DIFFRACTIONf_chiral_restr0.05212337
X-RAY DIFFRACTIONf_plane_restr0.0082867
X-RAY DIFFRACTIONf_dihedral_angle_d17.05716123
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.653271902465
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS0.557413443137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.42981090.42475600X-RAY DIFFRACTION87.67
2.57-2.660.36771430.40546284X-RAY DIFFRACTION98.98
2.66-2.750.42461270.38376306X-RAY DIFFRACTION99.27
2.75-2.860.39581560.37686309X-RAY DIFFRACTION99.45
2.86-2.990.34221450.33546347X-RAY DIFFRACTION99.27
2.99-3.150.32791380.30146334X-RAY DIFFRACTION99.26
3.15-3.350.32481170.27136404X-RAY DIFFRACTION99.5
3.35-3.610.27461340.23956339X-RAY DIFFRACTION99.54
3.61-3.970.26791430.20176358X-RAY DIFFRACTION99.48
3.97-4.540.20871380.1686415X-RAY DIFFRACTION99.8
4.54-5.720.20091240.16436486X-RAY DIFFRACTION99.97
5.72-44.940.18841600.16836589X-RAY DIFFRACTION99.79
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)
10.656149705918-0.2172833459740.3991126776560.701514377073-0.06672469534191.63879073615-0.0460422383261-0.440090501016-0.08219441905240.2598154582850.1439035143430.2125641368330.280975593242-0.660623624295-0.09373124081110.952972674308-0.09574764315850.03023249064071.082594897420.04153169308610.58283147664228.229-19.41485.825
20.900016153355-0.1891049403020.500373255120.28713150609-0.09884036677151.100625838760.0807998155403-0.550777417454-0.2190104778750.1117443853950.136889725150.2081438427250.46057059018-0.801034267265-0.1611739803610.890202585455-0.3618303934540.01282727633061.061662605860.1597005518450.64226514514513.016-29.81762.026
31.144329110720.212531549860.2740445972470.5414480224680.1896387067711.368357126090.09365974493920.234671549984-0.145729268363-0.02413161330150.01323035034140.08799737944010.603166140664-0.00941843195799-0.0854329205390.723440844902-0.13563220729-0.04513541998610.343929765801-0.006817522635710.52364698206338.689-26.87617.07
40.876926979779-0.1909264866530.3423507546520.545310305945-0.07243641750431.48074684056-0.0362949284606-0.07104419030170.08336096791690.03999102277820.08311348679680.04276371086130.0670119548941-0.270082995658-0.03985381145220.445256686517-0.105763417197-0.01070844481320.2978686377680.01338710166880.44511836895726.398-6.68235.558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )E4 - 480
2X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )E601 - 602
3X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )F601
4X-RAY DIFFRACTION2( CHAIN F AND RESID 2:523 )F2 - 523
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )A4 - 480
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )A601 - 602
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )B601
8X-RAY DIFFRACTION4( CHAIN B AND RESID 2:523 )B2 - 523

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