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- PDB-4wes: Nitrogenase molybdenum-iron protein from Clostridium pasteurianum... -

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Basic information

Entry
Database: PDB / ID: 4wes
TitleNitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution
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 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, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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 speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.08 Å
AuthorsZhang, L.M. / Morrison, C.N. / Kaiser, J.T. / Rees, D.C.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM45162 United States
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
National Science Foundation (NSF, United States)DGE-1144469 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 angstrom resolution: comparison with the Azotobacter vinelandii MoFe protein.
Authors: Zhang, L.M. / Morrison, C.N. / Kaiser, J.T. / Rees, D.C.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_nat / pdbx_audit_support ...entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / refine_hist / 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_alt_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_alt_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 / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)222,31513
Polymers218,7554
Non-polymers3,5599
Water44,7492484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24770 Å2
ΔGint-226 kcal/mol
Surface area61270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.701, 170.581, 87.540
Angle α, β, γ (deg.)90.00, 91.63, 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: 59202.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium pasteurianum (bacteria) / Strain: DSM 525 / References: UniProt: P00467, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 50175.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium pasteurianum (bacteria) / Strain: DSM 525 / References: UniProt: P11347, nitrogenase

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Non-polymers , 6 types, 2493 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-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2484 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8856, 1.734, 1.742
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2012 / Details: N2-cooled double focus KB mirrors
RadiationMonochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
21.7341
31.7421
ReflectionResolution: 1.08→38.93 Å / Num. obs: 842744 / % possible obs: 93 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.7
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 1.6 / % possible all: 88.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.08→38.93 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.854 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13287 16793 2 %RANDOM
Rwork0.11043 ---
obs0.11088 825717 92.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.45 Å2
2--0.08 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.08→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15133 0 104 2484 17721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916022
X-RAY DIFFRACTIONr_bond_other_d00.0215247
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.00222260
X-RAY DIFFRACTIONr_angle_other_deg0.886335392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04352073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90624.963673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.868152852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7071559
X-RAY DIFFRACTIONr_chiral_restr0.1080.22429
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117917
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2961.2277940
X-RAY DIFFRACTIONr_mcbond_other2.2961.2277939
X-RAY DIFFRACTIONr_mcangle_it2.6341.8489952
X-RAY DIFFRACTIONr_mcangle_other2.6341.8489953
X-RAY DIFFRACTIONr_scbond_it7.1811.658082
X-RAY DIFFRACTIONr_scbond_other7.1811.658083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2212.311728
X-RAY DIFFRACTIONr_long_range_B_refined11.03312.76921419
X-RAY DIFFRACTIONr_long_range_B_other11.03212.77121420
X-RAY DIFFRACTIONr_rigid_bond_restr6.769331269
X-RAY DIFFRACTIONr_sphericity_free93.6675513
X-RAY DIFFRACTIONr_sphericity_bonded21.493532799
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 1199 -
Rwork0.278 57592 -
obs--87.71 %

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