[English] 日本語
Yorodumi
- PDB-1n2c: NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n2c
TitleNITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE
Components
  • (NITROGENASE MOLYBDENUM-IRON ...) x 2
  • NITROGENASE IRON PROTEIN
KeywordsCOMPLEX OF NITROGENASE PROTEINS / NITROGENASE / NITROGEN FIXATION / SIGNAL TRANSDUCTION / ELECTRON TRANSFER / ATP HYDROLYSIS
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / : / 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 / TETRAFLUOROALUMINATE ION / FE-MO-S 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchindelin, H. / Kisker, C. / Rees, D.C.
CitationJournal: Nature / Year: 1997
Title: Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction.
Authors: Schindelin, H. / Kisker, C. / Schlessman, J.L. / Howard, J.B. / Rees, D.C.
History
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 21, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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 / _refine.ls_percent_reflns_obs / _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
Revision 1.5Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
F: NITROGENASE IRON PROTEIN
G: NITROGENASE IRON PROTEIN
H: NITROGENASE IRON PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,24830
Polymers354,9418
Non-polymers6,30722
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55490 Å2
ΔGint-452 kcal/mol
Surface area84850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 299.700, 334.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.983345, -0.051886, 0.174183), (-0.056575, -0.823381, -0.564662), (0.172717, -0.565112, 0.806733)5.04319, 180.69858, 56.00419
2given(-0.982758, -0.052821, 0.177192), (-0.057545, -0.823353, -0.564605), (0.175714, -0.565066, 0.806117)4.97166, 180.73842, 55.99032
3given(-0.880435, -0.467672, -0.078211), (-0.467474, 0.828502, 0.308307), (-0.079389, 0.308006, -0.948066)75.99072, 9.53609, 59.00141
4given(-0.979867, -0.06144, 0.18996), (-0.057419, -0.824547, -0.562872), (0.191214, -0.562447, 0.804419)5.27959, 180.66811, 56.00768
5given(0.875998, 0.466879, -0.121043), (0.481281, -0.829724, 0.282712), (0.03156, -0.305911, -0.951537)-58.78347, 135.23579, 112.32442

-
Components

-
NITROGENASE MOLYBDENUM-IRON ... , 2 types, 4 molecules ACBD

#1: Protein NITROGENASE MOLYBDENUM-IRON PROTEIN / NITROGENASE COMPONENT I / DINITROGENASE


Mass: 55231.848 Da / Num. of mol.: 2
Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS
Source method: isolated from a natural source / 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.: 2
Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS
Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

-
Protein , 1 types, 4 molecules EFGH

#3: Protein
NITROGENASE IRON PROTEIN / NITROGENASE COMPONENT II / NITROGENASE REDUCTASE


Mass: 31417.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: 2\:1 COMPLEX OF HOMODIMERIC FE-PROTEIN AND HETEROTETRAMERIC MOFE-PROTEIN
Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

-
Non-polymers , 8 types, 22 molecules

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


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical ChemComp-CFM / FE-MO-S CLUSTER


Mass: 775.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe7MoS9
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#10: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 6.5
Details: 16-20% PEG 8000, 0.1 M CACODYLATE PH 6.5 AND 20-50 MM MGCL2
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 %PEG800011
20.1 Mcacodylate11
320-50 mM11MgCl2

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 57735 / % possible obs: 73.8 % / Redundancy: 1.8 % / Rsym value: 0.098 / Net I/σ(I): 9.8
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.245 / % possible all: 28.8
Reflection
*PLUS
Num. measured all: 104037 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 28.8 % / Rmerge(I) obs: 0.245

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIN

1min
PDB Unreleased entry


Resolution: 3→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: ONE B-FACTOR PER RESIDUE / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -2 %RANDOM IN THIN SHELLS
Rwork0.208 ---
obs0.208 57735 73.8 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24190 0 142 0 24332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.011500
22X-RAY DIFFRACTION0.011500
33X-RAY DIFFRACTION0.011500
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more