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- PDB-5bvg: Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A.... -

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Basic information

Entry
Database: PDB / ID: 5bvg
TitleSelenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / nitrogenase / FeMo-cofactor / Se-incorporation
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-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 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 Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICG / IMIDAZOLE / SELENIUM ATOM / 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: 1.6 Å
AuthorsSpatzal, T. / Perez, K.A. / Howard, J.B. / Rees, D.C.
CitationJournal: Elife / Year: 2015
Title: Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.
Authors: Spatzal, T. / Perez, K.A. / Howard, J.B. / Rees, D.C.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
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_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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,18225
Polymers229,7964
Non-polymers4,38621
Water25,8151433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28410 Å2
ΔGint-167 kcal/mol
Surface area58950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.582, 130.825, 107.128
Angle α, β, γ (deg.)90.00, 108.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 55362.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / 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 natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 8 types, 1454 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-ICG / iron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated


Mass: 834.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS8Se
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1433 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe author indicates that UniProt annotation of residue 440 is incorrect.

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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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, NaCl, Imidazole/Malate, Sodiumdithionite

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→38.76 Å / Num. obs: 256394 / % possible obs: 97.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
SCALAdata scaling
Cootmodel building
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Q

3u7q


Resolution: 1.6→101.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.939 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17913 12691 5 %RANDOM
Rwork0.15156 ---
obs0.15292 243657 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.37 Å2
2---0.53 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→101.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15897 0 145 1433 17475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916903
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215752
X-RAY DIFFRACTIONr_angle_refined_deg1.531.98423323
X-RAY DIFFRACTIONr_angle_other_deg1.484336413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96952079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58424.036778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.519152945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5815100
X-RAY DIFFRACTIONr_chiral_restr0.0940.22406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5360.7248202
X-RAY DIFFRACTIONr_mcbond_other0.5360.7248201
X-RAY DIFFRACTIONr_mcangle_it0.6961.08610319
X-RAY DIFFRACTIONr_mcangle_other0.6961.08610320
X-RAY DIFFRACTIONr_scbond_it0.6650.818701
X-RAY DIFFRACTIONr_scbond_other0.6650.818702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.821.18512527
X-RAY DIFFRACTIONr_long_range_B_refined1.7816.74620756
X-RAY DIFFRACTIONr_long_range_B_other1.7816.74620757
X-RAY DIFFRACTIONr_rigid_bond_restr0.711332648
X-RAY DIFFRACTIONr_sphericity_free20.8135350
X-RAY DIFFRACTIONr_sphericity_bonded3.236533228
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 956 -
Rwork0.219 17961 -
obs--96.46 %
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)
10.35390.0945-0.05550.5017-0.01510.6348-0.019-0.05960.02180.0941-0.02660.02570-0.01610.04560.0491-0.00510.01290.0197-0.00850.0097-12.17156.920360.2921
20.2083-0.0123-0.11560.18370.07280.6486-0.05080.0187-0.05190.0394-0.03170.03550.1557-0.11020.08250.0691-0.03160.04260.0212-0.01830.0304-20.0323-11.081537.201
30.3231-0.0895-0.00810.5777-0.0670.4783-0.01060.0491-0.0333-0.0692-0.0185-0.05070.06920.03420.02910.02610.00170.01710.0154-0.00420.014310.0005-6.8548-4.5219
40.2523-0.0308-0.05070.22460.01850.5478-0.01070.02270.0201-0.0058-0.02120.0124-0.0511-0.06920.03190.01420.0024-0.00060.0126-0.00530.007-10.237311.24818.8787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 505
2X-RAY DIFFRACTION2B2 - 606
3X-RAY DIFFRACTION3C4 - 506
4X-RAY DIFFRACTION4D2 - 604

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