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- PDB-29un: Mo-Nitrogenase, MoFe protein, P1+ redox state, -200 mV -

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Basic information

Entry
Database: PDB / ID: 29un
TitleMo-Nitrogenase, MoFe protein, P1+ redox state, -200 mV
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Mo-Nitrogenase / MoFe protein / P1+ redox state / -200 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 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
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
G: Nitrogenase molybdenum-iron protein alpha chain
H: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,41950
Polymers465,5548
Non-polymers8,86542
Water26,4101466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.136, 156.823, 202.318
Angle α, β, γ (deg.)90.000, 89.985, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 248 or resid 250 through 480 or resid 601 through 608))
d_2ens_1(chain "C" and (resid 4 through 248 or resid 250 through 480 or resid 601 through 608))
d_3ens_1(chain "E" and (resid 4 through 248 or resid 250 through 480 or resid 601 through 608))
d_4ens_1(chain "G" and (resid 4 through 248 or resid 250 through 480 or resid 601 through 608))
d_1ens_2(chain "B" and (resid 2 through 370 or resid 372 through 523 or resid 606 through 607))
d_2ens_2(chain "D" and (resid 2 through 370 or resid 372 through 523 or resid 605 through 606))
d_3ens_2(chain "F" and (resid 2 through 370 or resid 372 through 523 or resid 606 through 607))
d_4ens_2(chain "H" and (resid 2 through 370 or resid 372 through 523 or resid 605 through 606))

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_1METMETARGARGAC4 - 24817 - 261
d_12ens_1VALVALGLUGLUAC250 - 480263 - 493
d_13ens_1HCAHCAHCAHCAAS502
d_14ens_1ICSICSICSICSAT503
d_15ens_11CL1CL1CL1CLBX602
d_21ens_1METMETARGARGCE4 - 24817 - 261
d_22ens_1VALVALGLUGLUCE250 - 480263 - 493
d_23ens_1HCAHCAHCAHCACDA601
d_24ens_1ICSICSICSICSCEA602
d_25ens_11CL1CL1CL1CLDGA601
d_31ens_1METMETARGARGEA4 - 24817 - 261
d_32ens_1VALVALGLUGLUEA250 - 480263 - 493
d_33ens_1HCAHCAHCAHCAEI601
d_34ens_1ICSICSICSICSEJ602
d_35ens_11CL1CL1CL1CLFL601
d_41ens_1METMETARGARGGG4 - 24817 - 261
d_42ens_1VALVALGLUGLUGG250 - 480263 - 493
d_43ens_1HCAHCAHCAHCAGOA601
d_44ens_1ICSICSICSICSGPA602
d_45ens_11CL1CL1CL1CLHRA601
d_11ens_2SERSERTRPTRPBD2 - 3702 - 370
d_12ens_2ASPASPARGARGBD372 - 523372 - 523
d_13ens_2GOLGOLGOLGOLBY603
d_14ens_2GOLGOLGOLGOLBZ604
d_21ens_2SERSERTRPTRPDF2 - 3702 - 370
d_22ens_2ASPASPARGARGDF372 - 523372 - 523
d_23ens_2GOLGOLGOLGOLDHA602
d_24ens_2GOLGOLGOLGOLDIA603
d_31ens_2SERSERTRPTRPFB2 - 3702 - 370
d_32ens_2ASPASPARGARGFB372 - 523372 - 523
d_33ens_2GOLGOLGOLGOLAR501
d_34ens_2GOLGOLGOLGOLFM602
d_41ens_2SERSERTRPTRPHH2 - 3702 - 370
d_42ens_2ASPASPARGARGHH372 - 523372 - 523
d_43ens_2GOLGOLGOLGOLHTA603
d_44ens_2GOLGOLGOLGOLHUA604

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999986395206, 0.00521503532176, 0.00011318309244), (0.00521483629887, -0.999984969974, 0.00169272231604), (0.000122008997963, -0.0016921090556, -0.999998560939)22.5251628954, -3.16668683079, -101.062066243
2given(-0.999984983098, -0.00547994082551, 6.18641796007E-5), (-0.00548000901788, 0.999984309581, -0.00116193543301), (-5.54958715098E-5, -0.0011622570006, -0.999999323039)-64.5775076755, -0.178840792292, -101.076259477
3given(-0.999999861116, 0.000378348865792, -0.000366907157056), (-0.000378426059347, -0.999999906275, 0.00021034328887), (-0.000366827539523, 0.000210482106887, 0.999999910567)-42.1598184909, -3.37993024391, -0.0254239124595
4given(0.999986417317, 0.0050570183704, -0.00126164428468), (0.00506074723289, -0.999982783575, 0.00297008260309), (-0.00124660280139, -0.00297642712422, -0.999994793418)22.4112987392, -3.0469928272, -101.065120301
5given(-0.999986049133, -0.00527115824608, -0.000341219702632), (-0.00527021681114, 0.999982457768, -0.00270351080113), (0.00035546435013, -0.002701674783, -0.999996287292)-64.6054828549, -0.307447599975, -101.018990196
6given(-0.999999669683, -4.19868335549E-5, 0.000811708098009), (4.22264832693E-5, -0.999999955529, 0.00029522636787), (0.000811695666291, 0.00029526054593, 0.999999626986)-42.0372839472, -3.34357316213, 0.0189132231381

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Components

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

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


Mass: 56852.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mo-Nitrogenase, MoFe protein, P1+ redox state, -200 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.: 4
Source method: isolated from a genetically manipulated source
Details: Mo-Nitrogenase, MoFe protein, P1+ redox state, -200 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 , 7 types, 1508 molecules

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


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


Mass: 787.451 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1466 / 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: 2.9 Å3/Da / Density % sol: 57.65 % / Description: Brown Diamond-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: I04 / Wavelength: 0.95375 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 2→202.22 Å / Num. obs: 348712 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 28.79 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.082 / Net I/σ(I): 5.5
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.99 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 17042 / CC1/2: 0.671 / Rpim(I) all: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→77.68 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 17446 5.02 %
Rwork0.1958 329866 -
obs0.1971 347312 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.22 Å2
Refinement stepCycle: LAST / Resolution: 2→77.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31856 0 328 1466 33650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007333035
X-RAY DIFFRACTIONf_angle_d0.89744790
X-RAY DIFFRACTIONf_chiral_restr0.04764672
X-RAY DIFFRACTIONf_plane_restr0.00755732
X-RAY DIFFRACTIONf_dihedral_angle_d15.504912270
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.368016692866
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.322726258543
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.295715975437
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.47534564348
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS0.3525156914
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS2.46936607802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.39616190.409110738X-RAY DIFFRACTION97.22
2.02-2.050.39225940.392410871X-RAY DIFFRACTION97.37
2.05-2.070.38345680.36110774X-RAY DIFFRACTION97.47
2.07-2.10.33965290.344611001X-RAY DIFFRACTION97.72
2.1-2.130.34096030.337410808X-RAY DIFFRACTION97.57
2.13-2.150.35136000.313110891X-RAY DIFFRACTION97.51
2.15-2.190.28715290.291710841X-RAY DIFFRACTION97.71
2.19-2.220.28955720.277210961X-RAY DIFFRACTION97.96
2.22-2.250.30295750.272310868X-RAY DIFFRACTION97.9
2.25-2.290.28845270.258710998X-RAY DIFFRACTION98.17
2.29-2.330.28466050.248610916X-RAY DIFFRACTION98.02
2.33-2.370.27075800.243410940X-RAY DIFFRACTION98.25
2.37-2.420.26925850.235910959X-RAY DIFFRACTION97.98
2.42-2.470.28385900.234910907X-RAY DIFFRACTION98.2
2.47-2.520.26115730.230410976X-RAY DIFFRACTION98.41
2.52-2.580.24135880.216111002X-RAY DIFFRACTION98.44
2.58-2.640.24175460.211411054X-RAY DIFFRACTION98.61
2.64-2.710.25895780.201110991X-RAY DIFFRACTION98.54
2.71-2.790.24295540.200610999X-RAY DIFFRACTION98.88
2.79-2.880.23475550.194711071X-RAY DIFFRACTION98.86
2.88-2.990.22385330.191711111X-RAY DIFFRACTION98.92
2.99-3.110.2266370.19411032X-RAY DIFFRACTION99.12
3.11-3.250.21465890.186411111X-RAY DIFFRACTION99.15
3.25-3.420.19795790.170611099X-RAY DIFFRACTION99.4
3.42-3.630.20376000.160811104X-RAY DIFFRACTION99.52
3.63-3.910.16715640.15311168X-RAY DIFFRACTION99.5
3.91-4.310.13586150.130311124X-RAY DIFFRACTION99.69
4.31-4.930.14926350.120711182X-RAY DIFFRACTION99.71
4.93-6.210.18176150.143211192X-RAY DIFFRACTION99.8
6.21-77.680.17286090.156611177X-RAY DIFFRACTION98.21
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)
10.803557833435-0.0126744204264-0.1180796566820.536964551028-0.03907265174191.3613807537-0.0414895393807-0.0463970503741-0.0502781108210.10275801442-0.0389251732405-0.02832765145020.04841770152040.05062122529390.07443147897530.2137835557480.01270660777060.005907333163370.2196975185940.03582295968690.238464790059-29.50229.323-15.646
20.439154625438-0.10883992558-0.01104376931150.367264429586-0.1128030679761.30738068567-0.009647004502510.1438386757450.0520413511703-0.015444035419-0.03100632890110.0598736312473-0.240465821894-0.3345871428620.04221665394380.209385506690.06024245252250.005342684546650.3292826982750.01656447820260.26534292829-45.25644.271-36.818
30.5994578934610.03065954256240.02741808753270.429767821854-0.003407638181581.414559514310.005635496714560.386478217493-0.0775876903058-0.154717802496-0.06612521055820.0314993061560.161274798926-0.05704644462560.05978648598540.3523614914290.04688000083040.0001013573323750.756746622104-0.04041342767070.309378467406-35.24229.209-85.462
40.371402656078-0.0363181199493-0.04509891921070.233761357098-0.03071054479531.51195943681-0.02182685230.2531573295050.0452795596009-0.0987000000381-0.0568724299136-0.054258287044-0.2346592883580.2980973230670.07411253725450.267745242269-0.008652664233-0.005029439269650.5381579472810.09121793768570.298134493786-19.56744.307-64.331
50.813683690538-0.02420637901850.04609751452980.5308196259020.05567499221791.38243216766-0.0469729867196-0.05862013382160.04776218214580.0808329814843-0.03527521878350.0285763363493-0.0545054562701-0.06392278764310.07270179304330.209548488394-0.0254808833037-0.01323583535080.226122496048-0.03123105568140.242050386494-12.574-32.704-15.654
60.463279152702-0.1176962953980.03659203789920.3969435129040.1164084509361.35536174784-0.011708709820.158253400821-0.0389659644024-0.010448989538-0.0248517298431-0.07018607827640.2082471735530.3129416963180.03695250509770.1885706530550.00913473526895-0.0006237278230060.320609334686-0.01655279596150.2578749194043.164-47.665-36.814
70.658673894825-0.014445210980.0388078498590.4712948179140.03570680027471.38855830084-0.0004173544811890.3759640534440.0824309260252-0.167879100412-0.0629719870298-0.0379299129564-0.1660099111390.04765355560570.06619756841170.3527896768650.004757484476590.01200054694490.7392696834180.04015983821450.299965049496-6.875-32.594-85.468
80.359229381923-0.04870550027420.02886299390690.2361766264180.02440125316661.54033746443-0.01943860428020.263180952783-0.0522017369031-0.0947157989237-0.06355844488070.05356506805250.247721403032-0.3295030959910.07523691470340.271975454543-0.05915680979580.008416771777330.54185481952-0.08821365844850.299150741451-22.538-47.692-64.342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 4:480 )E4 - 480
2X-RAY DIFFRACTION2( CHAIN F AND RESID 2:523 )F2 - 523
3X-RAY DIFFRACTION3( CHAIN A AND RESID 4:480 )A4 - 480
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:523 )B2 - 523
5X-RAY DIFFRACTION5( CHAIN C AND RESID 4:480 )C4 - 480
6X-RAY DIFFRACTION6( CHAIN D AND RESID 2:523 )D2 - 523
7X-RAY DIFFRACTION7( CHAIN G AND RESID 4:480 )G4 - 480
8X-RAY DIFFRACTION8( CHAIN H AND RESID 2:523 )H2 - 523

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