[English] 日本語
Yorodumi
- PDB-1g21: MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTE... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1g21
TitleMGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN
Components
  • (NITROGENASE MOLYBDENUM-IRON PROTEIN ...) x 2
  • NITROGENASE IRON PROTEIN
KeywordsOXIDOREDUCTASE / nitrogen-fixation / Fe protein / MoeFe protein / P-cluster / FeMo cofactor / 4Fe-4S
Function / homologyNitrogenase component 1, alpha chain / NifH/frxC family / P-loop containing nucleoside triphosphate hydrolase / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Nitrogenase component 1 type Oxidoreductase / Nitrogenase iron protein NifH / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1, conserved site ...Nitrogenase component 1, alpha chain / NifH/frxC family / P-loop containing nucleoside triphosphate hydrolase / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Nitrogenase component 1 type Oxidoreductase / Nitrogenase iron protein NifH / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1, conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / Domain of unknown function (DUF3364) / Nitrogenases component 1 alpha and beta subunits signature 2. / NifH/frxC family signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / NifH/chlL conserved site / 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 / Nitrogenase iron protein 1 / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Function and homology information
Specimen sourceAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3 Å resolution
AuthorsChiu, H.-J. / Peters, J.W. / Lanzilotta, W.N. / Ryle, M.J. / Seefeldt, L.C. / Howard, J.B. / Rees, D.C.
CitationJournal: Biochemistry / Year: 2001
Title: MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein.
Authors: Chiu, H. / Peters, J.W. / Lanzilotta, W.N. / Ryle, M.J. / Seefeldt, L.C. / Howard, J.B. / Rees, D.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 16, 2000 / Release: Jan 31, 2001
RevisionDateData content typeGroupProviderType
1.0Jan 31, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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)361,75326
Polyers355,5388
Non-polymers6,21518
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)52440
ΔGint (kcal/M)-433
Surface area (Å2)92110
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)110.5, 121.5, 264.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP 21 21 21
DetailsThe biological assembly is a dimer, and each subunit contains one MoeFe protein and two Fe protein monomers.

-
Components

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

#1: Protein/peptide NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN / E.C.1.18.6.1 / NITROGENASE COMPONENT I / DINITROGENASE / NIFD


Mass: 55363.043 Da / Num. of mol.: 2 / Source: (natural) Azotobacter vinelandii (bacteria) / Genus: Azotobacter / References: UniProt: P07328, nitrogenase
#2: Protein/peptide NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN / E.C.1.18.6.1 / NITROGENASE COMPONENT I / DINITROGENASE / NIFK


Mass: 59535.879 Da / Num. of mol.: 2 / Source: (natural) Azotobacter vinelandii (bacteria) / Genus: Azotobacter / References: UniProt: P07329, nitrogenase

-
Protein/peptide , 1 types, 4 molecules EFGH

#3: Protein/peptide
NITROGENASE IRON PROTEIN / E.C.1.18.6.1 / NITROGENASE COMPONENT II / NITROGENASE REDUCTASE / NIFH


Mass: 31435.084 Da / Num. of mol.: 4 / Source: (natural) Azotobacter vinelandii (bacteria) / Genus: Azotobacter / References: UniProt: P00459, nitrogenase

-
Non-polymers , 7 types, 18 molecules

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


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


Mass: 775.440 Da / Num. of mol.: 2 / Formula: Fe7MoS9
#6: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Formula: Fe8S7
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#9: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4 / Iron–sulfur cluster

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 / Density percent sol: 5 %
Crystal growTemp: 298 K / Method: microcapillary batch diffusion / pH: 8.5
Details: PEG 4000, sodium acetate, Tris-HCl. Ph 8.8, pH 8.5, microcapillary batch diffusion, temperature 298K
Crystal grow
*PLUS
Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
130 %PEG400011
20.2 M11NaOAc
30.1 MTris11
41 mMsodium dithionite11

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Apr 20, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionD resolution high: 3 Å / D resolution low: 2 Å / Number all: 52828 / Number obs: 51434 / Observed criterion sigma F: 1 / Observed criterion sigma I: 0.5 / Rmerge I obs: 0.132 / NetI over sigmaI: 12 / Redundancy: 7.3 % / Percent possible obs: 71.6
Reflection shellRmerge I obs: 0.282 / Highest resolution: 3 Å / Lowest resolution: 3.11 Å / Redundancy: 3 % / Percent possible all: 28.7
Reflection
*PLUS
Number measured all: 386858
Reflection shell
*PLUS
Percent possible obs: 28.7

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineStarting model: MoFe protein of nucleotide-free structure (PDB ID 1G20)
R Free selection details: thin shells / Cross valid method: THROUGHOUT / Sigma F: 1 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.285 / R factor R work: 0.238 / R factor all: 0.2466 / R factor obs: 0.2405 / Highest resolution: 3 Å / Lowest resolution: 2 Å / Number reflection R free: 2668 / Number reflection all: 52828 / Number reflection obs: 51434 / Percent reflection R free: 5 / Percent reflection obs: 71.6
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 23999 / Nucleic acid: 0 / Ligand: 238 / Solvent: 0 / Total: 24237
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_bond_d0.010
Software
*PLUS
Name: CNS / Classification: refinement
Refine
*PLUS
Sigma F: 1
Least-squares process
*PLUS
R factor obs: 0.238 / Highest resolution: 3 Å / Lowest resolution: 2 Å / Percent reflection R free: 5

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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