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- PDB-5bvh: CO-bound form of Selenium incorporated nitrogenase MoFe-protein (... -

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Basic information

Entry
Database: PDB / ID: 5bvh
TitleCO-bound form of Selenium incorporated nitrogenase MoFe-protein (Av1-Se-CO) 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 / carbonyl sulfide nitrogenase activity / 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 / CARBON MONOXIDE / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICH / Chem-ICS / IMIDAZOLE / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 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

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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)235,77326
Polymers229,7964
Non-polymers5,97722
Water32,6611813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33510 Å2
ΔGint-255 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.071, 130.833, 107.318
Angle α, β, γ (deg.)90.00, 110.64, 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 , 9 types, 1835 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
#5: Chemical ChemComp-ICH / iron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated


Mass: 928.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS6Se3
#6: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#9: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1813 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsIn the active site the multiple species are all co-existing, however, due to the limitations of the ...In the active site the multiple species are all co-existing, however, due to the limitations of the chemical component dictionary, they have been broken down into separate components.
Sequence detailsThe authors indicate that UniProt is incorrect in assigning residue 400 as Gln

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 %
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: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→38.71 Å / Num. obs: 301848 / % possible obs: 96.2 % / Redundancy: 7.2 % / Rsym value: 0.127 / Net I/σ(I): 11.3
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
SCALAdata scaling
XDSdata scaling
Cootmodel building
RefinementResolution: 1.53→100.43 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.468 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15971 14889 4.9 %RANDOM
Rwork0.14405 ---
obs0.14482 286922 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å20.03 Å2
2---0.04 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.53→100.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15883 0 176 1813 17872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916886
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215764
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.98523290
X-RAY DIFFRACTIONr_angle_other_deg1.529336441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07752078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70824.065770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.765152948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6891597
X-RAY DIFFRACTIONr_chiral_restr0.1180.22404
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119061
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023908
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_it0.591.078209
X-RAY DIFFRACTIONr_mcbond_other0.591.078206
X-RAY DIFFRACTIONr_mcangle_it0.9461.60310322
X-RAY DIFFRACTIONr_mcangle_other0.9461.60310323
X-RAY DIFFRACTIONr_scbond_it1.0221.1698677
X-RAY DIFFRACTIONr_scbond_other1.0221.1698678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6211.7112491
X-RAY DIFFRACTIONr_long_range_B_refined3.01410.5777489
X-RAY DIFFRACTIONr_long_range_B_other2.7510.2875408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 1031 -
Rwork0.23 21177 -
obs--95.9 %
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)
10.04180.02650.00870.07740.00960.09030.0116-0.0162-0.00480.0161-0.01610.00770.0103-0.02130.00450.0092-0.0018-0.00080.0163-0.00180.0032-29.0452-6.849554.4483
20.07210.0162-0.02960.01430.00580.16420.0055-0.01270.0038-0.0044-0.00170.0057-0.03890.0226-0.00380.0168-0.001-0.00410.0076-0.00370.005-8.245211.115441.4815
30.056-0.0311-0.02040.065-0.01420.11450.00990.01940.0066-0.0209-0.0185-0.0035-0.01220.00310.00860.01460.0017-0.00020.01220.00160.0026-4.90336.7271-9.832
40.0557-0.019-0.0320.0229-0.02690.1697-0.0099-0.0073-0.0091-0.0051-0.00960.00540.030.03210.01950.00760.00670.00250.0108-0.00110.00812.3341-11.212313.5042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 6496
2X-RAY DIFFRACTION2B2 - 6498
3X-RAY DIFFRACTION3C4 - 7496
4X-RAY DIFFRACTION4D2 - 7498

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