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- PDB-6n4l: Dithionite-reduced ADP-bound form of the nitrogenase Fe-protein f... -

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Basic information

Entry
Database: PDB / ID: 6n4l
TitleDithionite-reduced ADP-bound form of the nitrogenase Fe-protein from A. vinelandii
ComponentsNitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / nitrogenase / iron sulfur cluster / ADP
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 1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_symmetry / _struct_conn_type.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2204
Polymers31,4171
Non-polymers8033
Water4,810267
1
A: Nitrogenase iron protein 1
hetero molecules

A: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4408
Polymers62,8342
Non-polymers1,6066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area6050 Å2
ΔGint-87 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.587, 74.630, 75.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
DetailsThe biological unit contains an SF4, sitting on the crystallographic two-fold axis

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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.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAs-isolated, the protein has a 4Fe:4S cluster (SF4), sitting on the 2-fold axis

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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: 2.08 Å3/Da / Density % sol: 41.01 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% PEG 400, 0.17 mM Cymal 7, 0.1 M HEPES pH 7.5, 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: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.13→53.041 Å / Num. obs: 96897 / % possible obs: 100 % / Redundancy: 12.9 % / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Rsym value: 0.068 / Net I/av σ(I): 4.2 / Net I/σ(I): 17.6 / Num. measured all: 1246548
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
1.13-1.1911.90.7991167025139860.2390.8350.799399.9
1.19-1.26130.5431.4172439132640.1560.5660.5434.6100
1.26-1.3512.80.3852159874124470.1110.4010.3856.3100
1.35-1.4612.80.2483.1149651116550.0710.2580.2489.399.9
1.46-1.613.40.1485143652107080.0420.1540.14815.1100
1.6-1.7912.80.0957.412449597390.0270.0990.09522.299.9
1.79-2.0613.70.0669.311866386470.0180.0680.06633.7100
2.06-2.5312.60.05410.69253673570.0160.0560.05440.999.9
2.53-3.5713.50.05107760257610.0140.0520.0548.4100
3.57-39.01112.20.04910.64061133330.0140.0510.04949.599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5P

1g5p


Resolution: 1.13→39.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.066 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.157 4770 5 %RANDOM
Rwork0.1459 ---
obs0.1464 92016 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.59 Å2 / Biso mean: 16.113 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.13→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 32 268 2440
Biso mean--13.25 27.06 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172319
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6423290
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5785412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19923.361119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48315461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9391515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
X-RAY DIFFRACTIONr_rigid_bond_restr0.82234732
X-RAY DIFFRACTIONr_sphericity_free14.4035149
X-RAY DIFFRACTIONr_sphericity_bonded6.86554803
LS refinement shellResolution: 1.13→1.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 343 -
Rwork0.21 6735 -
all-7078 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -1.505 Å / Origin y: -4.1019 Å / Origin z: 13.3532 Å
111213212223313233
T0.0467 Å20.0118 Å20.0189 Å2-0.0052 Å20.0079 Å2--0.0215 Å2
L0.8978 °20.3379 °2-0.2728 °2-1.5509 °20.1931 °2--0.7425 °2
S0.0038 Å °-0.0128 Å °0.0453 Å °0.0332 Å °0.0039 Å °0.1088 Å °0.0475 Å °0.0076 Å °-0.0077 Å °

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