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- PDB-2x31: Modelling of the complex between subunits BchI and BchD of magnes... -

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Basic information

Entry
Database: PDB / ID: 2x31
TitleModelling of the complex between subunits BchI and BchD of magnesium chelatase based on single-particle cryo-EM reconstruction at 7.5 ang
DescriptorMAGNESIUM-CHELATASE 60 KDA SUBUNIT
MAGNESIUM-CHELATASE 38 KDA SUBUNIT
KeywordsLIGASE / BACTERIOCHLOROPHYLL BIOSYNTHESIS / PHOTOSYNTHESIS
Specimen sourceRhodobacter capsulatus / archaea / ロドバクター・カプスラータス
MethodElectron microscopy (7.5 Å resolution / Particle / Single particle)
AuthorsLunqvist, J. / Elmlund, H. / Peterson Wulff, R. / Berglund, L. / Elmlund, D. / Emanuelsson, C. / Hebert, H. / Willows, R.D. / Hansson, M. / Lindahl, M. / Al-Karadaghi, S.
CitationStructure, 2010, 18, 354-365

Structure, 2010, 18, 354-365 StrPapers
ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2010 / Release: Nov 10, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 10, 2010Structure modelrepositoryInitial release
1.1Mar 21, 2012Structure modelOther / Version format compliance
1.2Mar 20, 2013Structure modelDerived calculations / Refinement description
1.3Apr 19, 2017Structure modelOther

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Assembly

Deposited unit
A: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
B: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
C: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
D: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
E: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
F: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
G: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
H: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
I: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
J: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
K: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
L: MAGNESIUM-CHELATASE 38 KDA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)345,67912
Polyers345,67912
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
MAGNESIUM-CHELATASE 60 KDA SUBUNIT / MG-PROTOPORPHYRIN IX CHELATASE / MG-CHELATASE SUBUNIT D


Mass: 19666.758 Da / Num. of mol.: 6 / Fragment: RESIDUES 373-561
Source: (gene. exp.) Rhodobacter capsulatus / archaea / ロドバクター・カプスラータス
References: UniProt: P26175, EC: 6.6.1.1

Molecular function

Biological process

#2: Polypeptide(L)
MAGNESIUM-CHELATASE 38 KDA SUBUNIT / MG-PROTOPORPHYRIN IX CHELATASE


Mass: 37946.340 Da / Num. of mol.: 6
Source: (gene. exp.) Rhodobacter capsulatus / archaea / ロドバクター・カプスラータス
References: UniProt: P26239, EC: 6.6.1.1

Molecular function

Biological process

Sequence detailsHOMOLOGY MODEL OF INTEGRIN I DOMAINS OF SUBUBUNIT BCHD A,B,C,D,E,F SUBUNITS BCHI G,H,I,J,K,L BASED ON PDB ENTRY 1G8P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: BCHID COMPLEX OF RHODOBACTER CAPSULATUS MG CHELATASE / Type: COMPLEX
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 5.5 nm / Nominal defocus min: 1 nm / Cs: 2 mm
Image scansNumber digital images: 18
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C3
3D reconstructionResolution: 7.5 Å / Number of particles: 29400 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1G8P
Least-squares processHighest resolution: 7.5 Å
Refine hist #LASTHighest resolution: 7.5 Å
Number of atoms included #LASTProtein: 22890 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 22890

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