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- PDB-6bbl: Crystal structure of the a-96Gln MoFe protein variant in the pres... -

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Basic information

Entry
Database: PDB / ID: 6bbl
TitleCrystal structure of the a-96Gln MoFe protein variant in the presence of the substrate acetylene
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / Nitrogenase / N2 reduction / FeMo-cofactor / substrate binding / acetylene
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, OXIDIZED / acetylene / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / IMIDAZOLE / 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: 1.68 Å
AuthorsZadvornyy, O.A. / Keable, S.M. / Vertemara, J. / Eilers, B.J. / Karamatullah, D. / Rasmussen, A.J. / De Gioia, L. / Zampella, G. / Seefeldt, L.C. / Peters, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330807 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: Structural characterization of the nitrogenase molybdenum-iron protein with the substrate acetylene trapped near the active site.
Authors: Keable, S.M. / Vertemara, J. / Zadvornyy, O.A. / Eilers, B.J. / Danyal, K. / Rasmussen, A.J. / De Gioia, L. / Zampella, G. / Seefeldt, L.C. / Peters, J.W.
History
DepositionOct 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_nat / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _entity_src_nat.strain / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,46518
Polymers229,7404
Non-polymers3,72514
Water39,0932170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31100 Å2
ΔGint-189 kcal/mol
Surface area58540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.781, 128.251, 107.272
Angle α, β, γ (deg.)90.00, 109.11, 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 / Dinitrogenase / Nitrogenase component I


Mass: 55333.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ1264 / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ1264 / References: UniProt: P07329, nitrogenase

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Non-polymers , 8 types, 2184 molecules

#3: Chemical ChemComp-C2H / acetylene / ethyne


Mass: 26.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#6: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#7: Chemical ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2170 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8
Details: 30% w/v PEG4000, 0.1 M Tris, pH 8.0, 0.17 M sodium molybdate, 0.001 M sodium dithionite
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.68→49.9 Å / Num. obs: 204410 / % possible obs: 91.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 16.44 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.2
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.2 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(DEV_2880: ???)refinement
XDSdata reduction
HKL-2000data reduction
XSCALEdata scaling
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U7Q

3u7q


Resolution: 1.68→39.76 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 10163 4.97 %
Rwork0.151 --
obs0.153 204400 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15924 0 116 2170 18210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116475
X-RAY DIFFRACTIONf_angle_d2.45222373
X-RAY DIFFRACTIONf_dihedral_angle_d11.9549862
X-RAY DIFFRACTIONf_chiral_restr0.2262374
X-RAY DIFFRACTIONf_plane_restr0.0072863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6803-1.69940.26663070.23386385X-RAY DIFFRACTION90
1.6994-1.71940.2553450.22196547X-RAY DIFFRACTION94
1.7194-1.74030.24913520.20766645X-RAY DIFFRACTION94
1.7403-1.76240.25813300.20286544X-RAY DIFFRACTION94
1.7624-1.78560.23063770.19036597X-RAY DIFFRACTION94
1.7856-1.810.21413240.18786503X-RAY DIFFRACTION93
1.81-1.83590.22913150.18426251X-RAY DIFFRACTION88
1.8359-1.86330.23353050.17446431X-RAY DIFFRACTION91
1.8633-1.89240.20683660.17316606X-RAY DIFFRACTION95
1.8924-1.92340.21363690.16416694X-RAY DIFFRACTION94
1.9234-1.95660.19443650.15246524X-RAY DIFFRACTION94
1.9566-1.99220.18243610.14686665X-RAY DIFFRACTION95
1.9922-2.03050.18743600.14536661X-RAY DIFFRACTION95
2.0305-2.07190.16753470.14336682X-RAY DIFFRACTION95
2.0719-2.1170.18213770.14076645X-RAY DIFFRACTION95
2.117-2.16620.18773530.13846648X-RAY DIFFRACTION95
2.1662-2.22040.17463330.13966268X-RAY DIFFRACTION89
2.2204-2.28040.17263380.13346838X-RAY DIFFRACTION97
2.2804-2.34750.17193640.13176778X-RAY DIFFRACTION97
2.3475-2.42330.16673770.13426756X-RAY DIFFRACTION96
2.4233-2.50990.15943100.13326794X-RAY DIFFRACTION96
2.5099-2.61030.16623480.13716869X-RAY DIFFRACTION97
2.6103-2.72910.17953550.13356784X-RAY DIFFRACTION96
2.7291-2.8730.17693590.14286336X-RAY DIFFRACTION91
2.873-3.05290.17023610.14036845X-RAY DIFFRACTION97
3.0529-3.28850.16293540.14076549X-RAY DIFFRACTION93
3.2885-3.61920.17413170.14096398X-RAY DIFFRACTION90
3.6192-4.14250.15282440.14335245X-RAY DIFFRACTION74
4.1425-5.21720.18272450.1454966X-RAY DIFFRACTION70
5.2172-39.77290.22633050.18725783X-RAY DIFFRACTION80

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