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- PDB-2afi: Crystal Structure of MgADP bound Av2-Av1 Complex -

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Basic information

Entry
Database: PDB / ID: 2afi
TitleCrystal Structure of MgADP bound Av2-Av1 Complex
Components
  • (Nitrogenase molybdenum-iron ...) x 2
  • Nitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / Nitrogen fixation / Iron-sulfur / Metal-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 / 4 iron, 4 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 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. / Nitrogenase molybdenum-iron protein beta chain, N-terminal ...Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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. / 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 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FE(7)-MO-S(9)-N CLUSTER / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / IRON/SULFUR CLUSTER / Nitrogenase iron protein 1 / 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: 3.1 Å
AuthorsTezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C.
CitationJournal: Science / Year: 2005
Title: Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein
Authors: Tezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The Ca atom 2492 is associated with water molecules 9000, 9001, the Ca atom 4492 is ...HETEROGEN The Ca atom 2492 is associated with water molecules 9000, 9001, the Ca atom 4492 is associated with water molecules 9002, 9003, the Ca atom 6492 is associated with water molecules 9004, 9005 and the Ca atom 8492 is associated with water molecules 9006, 9007.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogenase molybdenum-iron protein
B: Nitrogenase molybdenum-iron protein
C: Nitrogenase molybdenum-iron protein
D: Nitrogenase molybdenum-iron protein
E: Nitrogenase iron protein 1
F: Nitrogenase iron protein 1
G: Nitrogenase iron protein 1
H: Nitrogenase iron protein 1
I: Nitrogenase molybdenum-iron protein
J: Nitrogenase molybdenum-iron protein
K: Nitrogenase molybdenum-iron protein
L: Nitrogenase molybdenum-iron protein
M: Nitrogenase iron protein 1
N: Nitrogenase iron protein 1
O: Nitrogenase iron protein 1
P: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)721,72952
Polymers709,88216
Non-polymers11,84636
Water1448
1
A: Nitrogenase molybdenum-iron protein
B: Nitrogenase molybdenum-iron protein
C: Nitrogenase molybdenum-iron protein
D: Nitrogenase molybdenum-iron protein
E: Nitrogenase iron protein 1
F: Nitrogenase iron protein 1
G: Nitrogenase iron protein 1
H: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,86426
Polymers354,9418
Non-polymers5,92318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Nitrogenase molybdenum-iron protein
J: Nitrogenase molybdenum-iron protein
K: Nitrogenase molybdenum-iron protein
L: Nitrogenase molybdenum-iron protein
M: Nitrogenase iron protein 1
N: Nitrogenase iron protein 1
O: Nitrogenase iron protein 1
P: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,86426
Polymers354,9418
Non-polymers5,92318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.915, 141.432, 165.549
Angle α, β, γ (deg.)73.69, 79.37, 76.58
Int Tables number1
Space group name H-MP1

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Components

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Nitrogenase molybdenum-iron ... , 2 types, 8 molecules ACIKBDJL

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


Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: alpha chain / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein
Nitrogenase molybdenum-iron protein / Nitrogenase component I / Dinitrogenase


Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: beta chain / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Protein , 1 types, 8 molecules EFGHMNOP

#3: Protein
Nitrogenase iron protein 1 / Nitrogenase component II / Nitrogenase Fe protein 1 / Nitrogenase reductase


Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

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Non-polymers , 8 types, 44 molecules

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


Mass: 206.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical
ChemComp-CFN / FE(7)-MO-S(9)-N CLUSTER


Mass: 789.447 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe7MoNS9
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.25 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG8000, Sodium Chloride, Magnesium Chloride, ADP, Dithionite, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 97281 / Num. obs: 97281 / % possible obs: 88.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 1.7 % / Rsym value: 0.075 / Net I/σ(I): 8.8
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.242 / % possible all: 72

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M1N, 2NIP

1m1n

2nip


Resolution: 3.1→49.43 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2770509.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The residues in the coordinates with 0 occupancy were not located in the experiments
RfactorNum. reflection% reflectionSelection details
Rfree0.27 9711 10 %RANDOM
Rwork0.229 ---
obs0.229 97281 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.5046 Å2 / ksol: 0.27916 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.61 Å2-0.92 Å2-5.44 Å2
2--7.37 Å2-14.3 Å2
3---2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48045 0 448 8 48501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.56
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.142
X-RAY DIFFRACTIONc_mcangle_it3.412.5
X-RAY DIFFRACTIONc_scbond_it2.942.5
X-RAY DIFFRACTIONc_scangle_it4.323
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 1210 9.2 %
Rwork0.294 11948 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5n2ase.parn2ase.top

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