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- PDB-6m2a: A non-His-rich type of chimeric sirohydrochlorin nickelochelatase... -

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Basic information

Entry
Database: PDB / ID: 6m2a
TitleA non-His-rich type of chimeric sirohydrochlorin nickelochelatase CfbA from M. jannaschii and M. barkeri
ComponentsSirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homology
Function and homology information


sirohydrochlorin nickelchelatase / sirohydrochlorin cobaltochelatase / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / methanogenesis / cobalt ion binding / nickel cation binding
Similarity search - Function
Sirohydrochlorin cobaltochelatase / : / Sirohydrochlorin cobaltochelatase CbiX-like / CbiX
Similarity search - Domain/homology
Sirohydrochlorin cobaltochelatase / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsFujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04639 Japan
CitationJournal: Chem Sci / Year: 2021
Title: The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.
Authors: Fujishiro, T. / Ogawa, S.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase
B: Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2234
Polymers28,0312
Non-polymers1922
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-68 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.210, 50.210, 90.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 126 / Label seq-ID: 1 - 126

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase / CbiXS / Sirohydrochlorin nickelchelatase


Mass: 14015.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This chimeric protein was prepared by substitution of the His-rich region of CfbA from Methanocaldococcus jannaschii by the corresponding non-His-rich region of CfbA from Methanosarcina barkeri.
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea), (gene. exp.) Methanosarcina barkeri (strain Fusaro / DSM 804) (archaea)
Gene: cbiX, cfbA, MJ0970, cbiX, cfbA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q58380, UniProt: P61816, sirohydrochlorin cobaltochelatase, sirohydrochlorin nickelchelatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1M ammonium sulfate, 0.3M Na-formate, 0.1M Tris, 3% (w/v) gamma-PGA, 10% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→43.48 Å / Num. obs: 12499 / % possible obs: 99.7 % / Redundancy: 9.289 % / Biso Wilson estimate: 45.688 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rrim(I) all: 0.184 / Χ2: 0.926 / Net I/σ(I): 8.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.23-2.336.4860.8791.7315520.8280.95697.8
2.33-2.438.9580.7552.4912740.9010.8100
2.43-2.539.7040.762.7811280.8850.802100
2.53-39.760.4644.7834100.9620.49100
3-49.9930.16912.6529620.9920.178100
4-59.1820.10519.1310720.9940.112100
5-610.1280.09820.314530.9950.103100
6-109.3950.0920.985090.9950.096100
10-43.4810.7740.08126.121370.9990.085100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XWS

2xws


Resolution: 2.23→43.48 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2.38 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2345 610 4.89 %
Rwork0.1932 --
obs0.1952 12484 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.51 Å2 / Biso mean: 43.5316 Å2 / Biso min: 22.51 Å2
Refinement stepCycle: final / Resolution: 2.23→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 10 18 1998
Biso mean--59.16 46.76 -
Num. residues----252
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1127X-RAY DIFFRACTION20.863TORSIONAL
12B1127X-RAY DIFFRACTION20.863TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.23-2.450.16361550.118929593114
2.46-2.810.20671580.161929993157
2.81-3.540.22891430.21329383081
3.54-43.480.2591540.205529793133

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