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- PDB-5cx1: Nitrogenase molybdenum-iron protein beta-K400E mutant -

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Basic information

Entry
Database: PDB / ID: 5cx1
TitleNitrogenase molybdenum-iron protein beta-K400E mutant
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Nitrogen fixation
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-ICS / 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: 1.7476 Å
AuthorsOwens, C.P. / Luca, M.A. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099813 United States
United States Department of Agriculture (USDA)2015-67012-22895 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis.
Authors: Owens, C.P. / Katz, F.E. / Carter, C.H. / Luca, M.A. / Tezcan, F.A.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
E: Nitrogenase molybdenum-iron protein alpha chain
F: Nitrogenase molybdenum-iron protein beta chain
G: Nitrogenase molybdenum-iron protein alpha chain
H: Nitrogenase molybdenum-iron protein beta chain
I: Nitrogenase molybdenum-iron protein alpha chain
J: Nitrogenase molybdenum-iron protein beta chain
K: Nitrogenase molybdenum-iron protein alpha chain
L: Nitrogenase molybdenum-iron protein beta chain
M: Nitrogenase molybdenum-iron protein alpha chain
N: Nitrogenase molybdenum-iron protein beta chain
O: Nitrogenase molybdenum-iron protein alpha chain
P: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)924,24548
Polymers910,60616
Non-polymers13,63932
Water190,38310568
1
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)231,06112
Polymers227,6514
Non-polymers3,4108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31530 Å2
ΔGint-253 kcal/mol
Surface area57840 Å2
MethodPISA
2
E: Nitrogenase molybdenum-iron protein alpha chain
F: Nitrogenase molybdenum-iron protein beta chain
G: Nitrogenase molybdenum-iron protein alpha chain
H: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,06112
Polymers227,6514
Non-polymers3,4108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31450 Å2
ΔGint-258 kcal/mol
Surface area58110 Å2
MethodPISA
3
I: Nitrogenase molybdenum-iron protein alpha chain
J: Nitrogenase molybdenum-iron protein beta chain
K: Nitrogenase molybdenum-iron protein alpha chain
L: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,06112
Polymers227,6514
Non-polymers3,4108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31520 Å2
ΔGint-253 kcal/mol
Surface area57710 Å2
MethodPISA
4
M: Nitrogenase molybdenum-iron protein alpha chain
N: Nitrogenase molybdenum-iron protein beta chain
O: Nitrogenase molybdenum-iron protein alpha chain
P: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,06112
Polymers227,6514
Non-polymers3,4108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31530 Å2
ΔGint-255 kcal/mol
Surface area57900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.502, 144.595, 177.747
Angle α, β, γ (deg.)90.00, 114.27, 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, 16 molecules ACEGIKMOBDFHJLNP

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


Mass: 54289.906 Da / Num. of mol.: 8 / 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: 59535.816 Da / Num. of mol.: 8 / Mutation: K400D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 10600 molecules

#3: Chemical
ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H10O7
#4: Chemical
ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CFe7MoS9
#5: Chemical
ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe8S7
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10568 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris pH 8, 600 mM NaCl, 18% PEG 10000, 5 mM sodium dithionite

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7476→39.01 Å / Num. obs: 793848 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7476→1.78 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692phasing
Cootmodel building
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1N

1m1n


Resolution: 1.7476→38.682 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 77589 9.97 %
Rwork0.1979 --
obs0.2026 777946 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7476→38.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63636 0 384 10568 74588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01266039
X-RAY DIFFRACTIONf_angle_d1.5390964
X-RAY DIFFRACTIONf_dihedral_angle_d13.29824740
X-RAY DIFFRACTIONf_chiral_restr0.0749446
X-RAY DIFFRACTIONf_plane_restr0.00811426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7476-1.76750.284222360.218120235X-RAY DIFFRACTION83
1.7675-1.78830.269125920.204523454X-RAY DIFFRACTION96
1.7883-1.81010.253725580.199622972X-RAY DIFFRACTION95
1.8101-1.8330.260226970.19523958X-RAY DIFFRACTION98
1.833-1.85710.239426930.18523896X-RAY DIFFRACTION99
1.8571-1.88260.319626480.269323807X-RAY DIFFRACTION98
1.8826-1.90950.365925010.312622554X-RAY DIFFRACTION92
1.9095-1.9380.486723090.455920955X-RAY DIFFRACTION86
1.938-1.96830.320826850.253323667X-RAY DIFFRACTION98
1.9683-2.00050.230527360.169423948X-RAY DIFFRACTION98
2.0005-2.0350.227126240.169424003X-RAY DIFFRACTION98
2.035-2.0720.306521280.249219435X-RAY DIFFRACTION80
2.072-2.11190.279525450.205322618X-RAY DIFFRACTION93
2.1119-2.1550.230225840.172423308X-RAY DIFFRACTION95
2.155-2.20180.226925620.170323491X-RAY DIFFRACTION96
2.2018-2.2530.370824460.302522886X-RAY DIFFRACTION93
2.253-2.30940.280225750.212223134X-RAY DIFFRACTION95
2.3094-2.37180.222527060.167424068X-RAY DIFFRACTION99
2.3718-2.44160.223726750.168623983X-RAY DIFFRACTION99
2.4416-2.52040.222626730.171524117X-RAY DIFFRACTION99
2.5204-2.61050.227127260.17324208X-RAY DIFFRACTION99
2.6105-2.71490.265525780.211723641X-RAY DIFFRACTION97
2.7149-2.83850.235725310.181523235X-RAY DIFFRACTION95
2.8385-2.98810.224625960.177124307X-RAY DIFFRACTION99
2.9881-3.17520.222327010.180924210X-RAY DIFFRACTION99
3.1752-3.42020.214726780.179424201X-RAY DIFFRACTION99
3.4202-3.76420.227226020.194723994X-RAY DIFFRACTION98
3.7642-4.30820.21225720.17723388X-RAY DIFFRACTION95
4.3082-5.42550.186327110.15624486X-RAY DIFFRACTION99
5.4255-38.69150.19927210.175924198X-RAY DIFFRACTION97

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