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- PDB-3k1a: Insights into substrate binding at FeMo-cofactor in nitrogenase f... -

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Basic information

Entry
Database: PDB / ID: 3k1a
TitleInsights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / NITROGEN FIXATION / MoFe protein / nitrogenase / isoleucine / proton reduction / nitrogen / acetylene / hydride reduction / ATP-binding / Iron / Iron-sulfur / Metal-binding / Nucleotide-binding / Molybdenum
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(7)-MO-S(9)-N CLUSTER / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / 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: 2.23 Å
AuthorsPeters, J.W. / Sarma, R. / Barney, B.M. / Keable, S. / Seefeldt, L.C. / Dean, D.R.
CitationJournal: J.Inorg.Biochem. / Year: 2010
Title: Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant
Authors: Sarma, R. / Barney, B.M. / Keable, S. / Dean, D.R. / Seefeldt, L.C. / Peters, J.W.
History
DepositionSep 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)232,71512
Polymers229,3014
Non-polymers3,4148
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28710 Å2
ΔGint-163.8 kcal/mol
Surface area58150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.019, 129.458, 107.088
Angle α, β, γ (deg.)90.00, 109.01, 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 / Nitrogenase component I / Dinitrogenase


Mass: 55245.875 Da / Num. of mol.: 2 / Mutation: V70I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifDK, nifK / Production host: Escherichia coli (E. coli) / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component I / Dinitrogenase


Mass: 59404.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: Escherichia coli (E. coli) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 838 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-CFN / FE(7)-MO-S(9)-N CLUSTER


Mass: 789.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe7MoNS9
#5: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: 30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.89 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 187881 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 3.8 % / Rsym value: 0.115 / Net I/σ(I): 11.8
Reflection shellResolution: 2.23→2.33 Å / Redundancy: 3.5 % / Num. unique all: 18797 / Rsym value: 0.233

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MIN
Resolution: 2.23→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.233 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25433 4778 5 %RANDOM
Rwork0.20449 ---
obs0.207 90665 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.399 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20.38 Å2
2--0.23 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15778 0 96 830 16704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02216354
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211219
X-RAY DIFFRACTIONr_angle_refined_deg3.2261.97722335
X-RAY DIFFRACTIONr_angle_other_deg1.279327295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81151973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46924.108757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.597152844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5931591
X-RAY DIFFRACTIONr_chiral_restr0.060.22323
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023329
X-RAY DIFFRACTIONr_nbd_refined0.190.23803
X-RAY DIFFRACTIONr_nbd_other0.1910.212772
X-RAY DIFFRACTIONr_nbtor_refined0.1730.27989
X-RAY DIFFRACTIONr_nbtor_other0.0820.27994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2834
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2370.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.23
X-RAY DIFFRACTIONr_mcbond_it2.29610205
X-RAY DIFFRACTIONr_mcbond_other0.37264030
X-RAY DIFFRACTIONr_mcangle_it2.138815829
X-RAY DIFFRACTIONr_scbond_it5.386157220
X-RAY DIFFRACTIONr_scangle_it7.743306116
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 320 -
Rwork0.273 5447 -
obs--80.57 %

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