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- PDB-3pdi: Precursor bound NifEN -

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Basic information

Entry
Database: PDB / ID: 3pdi
TitlePrecursor bound NifEN
Components
  • Nitrogenase MoFe cofactor biosynthesis protein NifE
  • Nitrogenase MoFe cofactor biosynthesis protein NifN
KeywordsPROTEIN BINDING / Nitrogenase Cofactor maturation / NifB / NifDK / NifH
Function / homology
Function and homology information


nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / protein-containing complex assembly / metal ion binding
Similarity search - Function
Nitrogenase MoFe cofactor biosynthesis protein NifE, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1090 / Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / 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 MoFe cofactor biosynthesis protein NifE, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1090 / Nitrogenase MoFe cofactor biosynthesis protein NifE / Nitrogenase molybdenum-iron cofactor biosynthesis protein / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-Cluster (Fe8S9) / IRON/SULFUR CLUSTER / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifE / Nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement/SAD / Resolution: 2.4 Å
AuthorsKaiser, J.T. / Hu, Y. / Wiig, J.A. / Rees, D.C. / Ribbe, M.W.
CitationJournal: Science / Year: 2011
Title: Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase.
Authors: Kaiser, J.T. / Hu, Y. / Wiig, J.A. / Rees, D.C. / Ribbe, M.W.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase MoFe cofactor biosynthesis protein NifE
B: Nitrogenase MoFe cofactor biosynthesis protein NifN
C: Nitrogenase MoFe cofactor biosynthesis protein NifE
D: Nitrogenase MoFe cofactor biosynthesis protein NifN
E: Nitrogenase MoFe cofactor biosynthesis protein NifE
F: Nitrogenase MoFe cofactor biosynthesis protein NifN
G: Nitrogenase MoFe cofactor biosynthesis protein NifE
H: Nitrogenase MoFe cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,76616
Polymers409,3948
Non-polymers4,3728
Water00
1
A: Nitrogenase MoFe cofactor biosynthesis protein NifE
B: Nitrogenase MoFe cofactor biosynthesis protein NifN
C: Nitrogenase MoFe cofactor biosynthesis protein NifE
D: Nitrogenase MoFe cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8838
Polymers204,6974
Non-polymers2,1864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-118 kcal/mol
Surface area60320 Å2
MethodPISA
2
E: Nitrogenase MoFe cofactor biosynthesis protein NifE
F: Nitrogenase MoFe cofactor biosynthesis protein NifN
G: Nitrogenase MoFe cofactor biosynthesis protein NifE
H: Nitrogenase MoFe cofactor biosynthesis protein NifN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8838
Polymers204,6974
Non-polymers2,1864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15660 Å2
ΔGint-119 kcal/mol
Surface area60410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.070, 95.220, 149.980
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 4:435 )
211CHAIN D AND (RESSEQ 4:435 )
311CHAIN F AND (RESSEQ 4:435 )
411CHAIN H AND (RESSEQ 4:435 )
112CHAIN A AND (RESSEQ 24:450 )
212CHAIN C AND (RESSEQ 24:450 )
312CHAIN E AND (RESSEQ 24:450 )
412CHAIN G AND (RESSEQ 24:450 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Nitrogenase MoFe cofactor biosynthesis protein NifE


Mass: 53046.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: Avin_01450, nifE / Production host: Azotobacter Vinelandii (bacteria) / References: UniProt: C1DH03
#2: Protein
Nitrogenase MoFe cofactor biosynthesis protein NifN


Mass: 49301.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: Avin_01470, nifN / Production host: Azotobacter Vinelandii (bacteria) / References: UniProt: C1DH04
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-CZL / L-Cluster (Fe8S9)


Mass: 741.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8H6S9

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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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 297 K / Method: liquid diffusion / pH: 7.5
Details: 20% PEG 3350, 0.2M Magnersium Nitrate, pH 7.5, LIQUID DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033, 1.738
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 25, 2008
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.7381
ReflectionResolution: 2.4→40 Å / Num. obs: 139605 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.4274 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: molecular replacement/SAD / Resolution: 2.4→39.829 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 40.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3407 13820 9.9 %
Rwork0.2944 --
obs0.299 139605 87.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.368 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8036 Å2-0 Å20.1782 Å2
2---0.9887 Å20 Å2
3---1.7922 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26012 0 100 0 26112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01326640
X-RAY DIFFRACTIONf_angle_d1.70536252
X-RAY DIFFRACTIONf_dihedral_angle_d20.3979740
X-RAY DIFFRACTIONf_chiral_restr0.1144128
X-RAY DIFFRACTIONf_plane_restr0.0084740
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3223X-RAY DIFFRACTIONPOSITIONAL
12D3223X-RAY DIFFRACTIONPOSITIONAL0.069
13F3223X-RAY DIFFRACTIONPOSITIONAL0.065
14H3223X-RAY DIFFRACTIONPOSITIONAL0.067
21A3280X-RAY DIFFRACTIONPOSITIONAL
22C3280X-RAY DIFFRACTIONPOSITIONAL0.06
23E3280X-RAY DIFFRACTIONPOSITIONAL0.058
24G3280X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42740.3955660.2965625X-RAY DIFFRACTION13
2.4274-2.45590.35461360.30411248X-RAY DIFFRACTION26
2.4559-2.48590.38311970.33951810X-RAY DIFFRACTION38
2.4859-2.51730.3552360.35482347X-RAY DIFFRACTION48
2.5173-2.55050.38852990.36622922X-RAY DIFFRACTION61
2.5505-2.58540.38973570.36273334X-RAY DIFFRACTION69
2.5854-2.62230.39984570.3413787X-RAY DIFFRACTION80
2.6223-2.66150.39694650.33824229X-RAY DIFFRACTION88
2.6615-2.7030.39645040.33374587X-RAY DIFFRACTION96
2.703-2.74730.38675010.33124687X-RAY DIFFRACTION98
2.7473-2.79470.36865280.33274713X-RAY DIFFRACTION98
2.7947-2.84550.37654780.31434797X-RAY DIFFRACTION99
2.8455-2.90020.38055240.31714781X-RAY DIFFRACTION99
2.9002-2.95940.37515660.32234762X-RAY DIFFRACTION100
2.9594-3.02370.35555200.31634774X-RAY DIFFRACTION100
3.0237-3.0940.37815100.32294790X-RAY DIFFRACTION100
3.094-3.17140.37255640.33344809X-RAY DIFFRACTION100
3.1714-3.25710.35765210.33494764X-RAY DIFFRACTION100
3.2571-3.35290.39945270.32164823X-RAY DIFFRACTION100
3.3529-3.46110.36815400.31144783X-RAY DIFFRACTION100
3.4611-3.58470.37035160.32114825X-RAY DIFFRACTION100
3.5847-3.72810.41615270.34254732X-RAY DIFFRACTION98
3.7281-3.89760.32225530.27814770X-RAY DIFFRACTION100
3.8976-4.10290.3165410.27434811X-RAY DIFFRACTION100
4.1029-4.35970.3115420.2664832X-RAY DIFFRACTION100
4.3597-4.69580.28125270.24934852X-RAY DIFFRACTION100
4.6958-5.16750.29985300.25124832X-RAY DIFFRACTION100
5.1675-5.91320.30045450.26014865X-RAY DIFFRACTION100
5.9132-7.4420.30455240.25724893X-RAY DIFFRACTION100
7.442-39.83450.25795190.2285001X-RAY DIFFRACTION100

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