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- PDB-6q93: MgADP-bound Fe protein of Vanadium nitrogenase from Azotobacter v... -

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Basic information

Entry
Database: PDB / ID: 6q93
TitleMgADP-bound Fe protein of Vanadium nitrogenase from Azotobacter vinelandii
ComponentsNitrogenase iron protein
KeywordsELECTRON TRANSPORT / Biological nitrogen fixation / Dinitrogenase reductase / Vanadium nitrogenase / Fe protein / VnfH
Function / homology
Function and homology information


nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Nitrogenase iron protein
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRohde, M. / Gerhardt, S. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council310656 Germany
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Crystal structure of VnfH, the iron protein component of vanadium nitrogenase.
Authors: Rohde, M. / Trncik, C. / Sippel, D. / Gerhardt, S. / Einsle, O.
History
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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.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 iron protein
B: Nitrogenase iron protein
C: Nitrogenase iron protein
D: Nitrogenase iron protein
E: Nitrogenase iron protein
F: Nitrogenase iron protein
G: Nitrogenase iron protein
H: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,55330
Polymers248,4858
Non-polymers5,06722
Water7,008389
1
A: Nitrogenase iron protein
B: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3767
Polymers62,1212
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-74 kcal/mol
Surface area20180 Å2
MethodPISA
2
C: Nitrogenase iron protein
D: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4008
Polymers62,1212
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-86 kcal/mol
Surface area20170 Å2
MethodPISA
3
E: Nitrogenase iron protein
F: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4008
Polymers62,1212
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-75 kcal/mol
Surface area19950 Å2
MethodPISA
4
G: Nitrogenase iron protein
H: Nitrogenase iron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3767
Polymers62,1212
Non-polymers1,2555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-78 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.573, 176.857, 354.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Nitrogenase iron protein / Nitrogenase Fe protein / Nitrogenase component II / Nitrogenase reductase


Mass: 31060.686 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / References: UniProt: C1DI30, nitrogenase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris/HCl buffer, magnesium chloride, ADP, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.54 Å / Num. obs: 150174 / % possible obs: 99.9 % / Redundancy: 27.8 % / Biso Wilson estimate: 46.59 Å2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FP6
Resolution: 2.2→49.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7601 5.06 %RANDOM
Rwork0.2 ---
obs0.201 150093 99.9 %-
Displacement parametersBiso mean: 68.75 Å2
Baniso -1Baniso -2Baniso -3
1-8.734 Å20 Å20 Å2
2---14.1316 Å20 Å2
3---5.3976 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16541 0 258 389 17188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00917027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1223012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6097SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3020HARMONIC5
X-RAY DIFFRACTIONt_it17027HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2249SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19936SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.21 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2717 155 5.16 %
Rwork0.2324 2847 -
all0.2345 3002 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.49760.2927-0.06522.25170.40043.33750.08320.0489-0.06290.2412-0.0464-0.1122-0.1537-0.099-0.0368-0.02580.07960.0185-0.06910.0162-0.1083-12.605-32.5497-17.4172
22.5341-1.8287-0.1820-0.78851.6465-0.2455-0.14590.54180.3923-0.0504-0.5442-0.36370.38990.2959-0.11960.0442-0.1449-0.3040.04620.3046.1315-13.7204-27.9895
32.45090.3414-1.11830.612-0.75314.4432-0.10620.5442-0.03130.02290.07580.0134-0.1247-0.32030.0304-0.304-0.002-0.01460.2036-0.0302-0.2509-17.2673-44.9973-68.653
41.76910.7411-0.61052.5279-1.12452.3643-0.23090.1938-0.5442-0.07280.0826-0.41120.3584-0.06780.1483-0.23640.07550.0339-0.0711-0.07490.053-22.307-65.1861-49.9604
52.6191-0.2818-0.66461.3247-0.15661.48230.1552-0.12-0.01970.5442-0.13730.54420.3434-0.0265-0.01790.09850.01120.152-0.304-0.0880.11966.3954-80.9164-26.7316
60.92060.00840.44293.5646-0.18812.67150.01960.00990.00920.5008-0.21270.16270.0273-0.02440.193-0.02340.0640.0334-0.1079-0.0217-0.132525.9211-61.2672-18.5171
72.10010.59260.66022.31730.56262.40130.07290.36150.54420.18590.05620.2032-0.17230.0936-0.1291-0.24740.08680.0687-0.02740.13490.021934.4188-30.2986-52.0782
83.0780.46430.73010.79190.8113.4705-0.07730.5442-0.01230.10340.1781-0.03570.33630.5149-0.1008-0.3040.0729-0.00570.27470.0261-0.282930.3824-50.5172-70.6813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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