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- PDB-6n4k: Dithionite-reduced nucleotide-free form of the nitrogenase Fe-pro... -

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Basic information

Entry
Database: PDB / ID: 6n4k
TitleDithionite-reduced nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii
ComponentsNitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / nitrogenase / iron sulfur cluster
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
IRON/SULFUR CLUSTER / Nitrogenase iron protein 1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.756 Å
AuthorsWenke, B.B. / Spatzal, T. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM045162 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0States of the Nitrogenase Fe-Protein.
Authors: Wenke, B.B. / Spatzal, T. / Rees, D.C.
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
B: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1863
Polymers62,8342
Non-polymers3521
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-35 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.620, 45.199, 108.772
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31417.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: of 40% PEG 1000, 0.2 M NaCl, 0.1 M MES/OH pH 6.5, 10% 2,2,2-trifluoroethanol, 5 mM dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.756→108.055 Å / Num. obs: 48484 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Rsym value: 0.045 / Net I/av σ(I): 7.9 / Net I/σ(I): 22 / Num. measured all: 323888
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.756-1.855.70.2083.63387359120.0920.2280.2085.981.8
1.85-1.966.90.1563.74745668980.0640.1690.1569.899.1
1.96-2.16.60.1046.34227163620.0430.1130.10413.798.8
2.1-2.276.90.0797.84148260300.0320.0850.07918.699.3
2.27-2.486.80.059113764955220.0240.0640.05923.199.2
2.48-2.786.80.052123380349740.0210.0560.05226.998.6
2.78-3.216.90.04214.33076344680.0170.0460.04233.499.4
3.21-3.936.90.03814.92573537380.0150.0410.0384198.7
3.93-5.556.80.03416.11975329240.0140.0370.03445.398.6
5.55-39.2576.70.0411.31110316560.0170.0430.0442.798.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0232refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5P

1g5p


Resolution: 1.756→39.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.903 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2369 4.9 %RANDOM
Rwork0.1708 ---
obs0.1729 46085 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.53 Å2 / Biso mean: 31.362 Å2 / Biso min: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.84 Å2
2--0.67 Å20 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.756→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 8 46 4147
Biso mean--18.52 30.84 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134120
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173912
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6425565
X-RAY DIFFRACTIONr_angle_other_deg1.5971.5759067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7223.467199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42715736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1111524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_rigid_bond_restr1.28338031
X-RAY DIFFRACTIONr_sphericity_free21.645536
X-RAY DIFFRACTIONr_sphericity_bonded12.07157990
LS refinement shellResolution: 1.756→1.801 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 110 -
Rwork0.178 2307 -
all-2417 -
obs--65.57 %
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)
11.85-0.4678-0.31611.8368-0.06622.28680.05770.1058-0.08360.1713-0.01950.03130.0754-0.0014-0.03820.02760.0032-0.00740.01-0.0120.1015-18.1734-11.822636.5903
23.61211.0423-0.55442.90910.29941.8339-0.10140.3588-0.0864-0.32450.0480.02620.0107-0.0240.05340.03970.0111-0.00520.1284-0.02960.0481-40.1541-8.642417.6813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 271
2X-RAY DIFFRACTION2B1 - 271

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