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- PDB-6m25: Sirohydrochlorin nickelochelatase CfbA in P41 space group -

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Basic information

Entry
Database: PDB / ID: 6m25
TitleSirohydrochlorin nickelochelatase CfbA in P41 space group
ComponentsSirohydrochlorin 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
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Assembly

Deposited unit
A: Sirohydrochlorin cobaltochelatase
B: Sirohydrochlorin cobaltochelatase


Theoretical massNumber of molelcules
Total (without water)33,1082
Polymers33,1082
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-31 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.550, 68.550, 82.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 143 / Label seq-ID: 1 - 143

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Sirohydrochlorin cobaltochelatase / CbiXS / Sirohydrochlorin nickelchelatase


Mass: 16554.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: cbiX, cfbA, MJ0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q58380, sirohydrochlorin cobaltochelatase, sirohydrochlorin nickelchelatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
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, 5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→68.55 Å / Num. all: 13290 / Num. obs: 13290 / % possible obs: 100 % / Redundancy: 11.8 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.248 / Rsym value: 0.237 / Net I/av σ(I): 2 / Net I/σ(I): 6.9 / Num. measured all: 156207
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
2.5-2.64110.7740.92118719300.2440.8120.7742.8
2.64-2.810.90.5971.11964118090.1890.6260.5973.6
2.8-2.9912.90.4321.52210917150.1250.450.4325.1
2.99-3.2312.60.32822012316020.0960.3420.3286.8
3.23-3.5411.90.2822.21756414820.0850.2950.2828.1
3.54-3.9510.60.2432.71413513390.0780.2550.2438.9
3.95-4.5612.40.2093.11467711850.0610.2180.20910.8
4.56-5.5912.70.1983.2126509930.0570.2060.19811
5.59-7.9111.10.1983.187107830.0630.2080.1989.6
7.91-82.41120.1723.254114520.0510.1790.17211

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XWS

2xws


Resolution: 2.5→68.55 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.438 / SU ML: 0.154 / SU R Cruickshank DPI: 0.0709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.051 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 698 5.3 %RANDOM
Rwork0.208 ---
obs0.2099 12565 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.33 Å2 / Biso mean: 52.598 Å2 / Biso min: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 2.5→68.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 14 1934
Biso mean---62.22 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121950
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6372636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34621100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.30415370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9781518
X-RAY DIFFRACTIONr_chiral_restr0.1170.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021448
Refine LS restraints NCS

Ens-ID: 1 / Number: 3378 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 48 -
Rwork0.199 906 -
all-954 -
obs--99.9 %

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