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- PDB-8i55: Wild-type CfbA at 1.99 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 8i55
TitleWild-type CfbA at 1.99 angstrom resolution
ComponentsSirohydrochlorin cobaltochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase / Nickel
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 DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsOgawa, S. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04639 Japan
CitationJournal: Protein Sci. / Year: 2024
Title: Structural insights into the recognition of tetrapyrrole substrates by ancestral class II chelatase CfbA.
Authors: Ogawa, S. / Hikita, M. / Fujishiro, T.
History
DepositionJan 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 67.720, 82.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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 DSM 2661 (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.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.3M Na-malonate, 0.1M Tris-HCl, 8% (w/v) Gamma-PGA

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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: Jun 1, 2021
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 25589 / % possible obs: 100 % / Redundancy: 9.44 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Net I/σ(I): 14.87
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.99-2.090.99934880.7561.0641
2.09-2.190.56128590.9060.5961
2.19-2.30.36626190.9570.3861
2.3-2.50.22336550.9840.2351
2.5-30.11554250.9960.1211
3-3.50.07327690.9970.0771
3.5-40.06415730.9960.0681
4-50.06415430.9970.0681
5-60.0646970.9970.0681
6-100.0737460.9960.0771
10-500.082150.9910.0851

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→47.89 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1279 5 %
Rwork0.1803 --
obs0.1814 25575 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 0 79 1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091935
X-RAY DIFFRACTIONf_angle_d1.4882618
X-RAY DIFFRACTIONf_dihedral_angle_d33.548262
X-RAY DIFFRACTIONf_chiral_restr0.086309
X-RAY DIFFRACTIONf_plane_restr0.01336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.070.30731420.26362692X-RAY DIFFRACTION100
2.07-2.160.27281410.21822686X-RAY DIFFRACTION100
2.16-2.280.22911410.19462673X-RAY DIFFRACTION100
2.28-2.420.2431420.18582700X-RAY DIFFRACTION100
2.42-2.610.20071420.19322705X-RAY DIFFRACTION100
2.61-2.870.27221420.20882689X-RAY DIFFRACTION100
2.87-3.280.17261420.18412697X-RAY DIFFRACTION100
3.29-4.140.1931430.15812708X-RAY DIFFRACTION100
4.14-47.890.18291440.17312746X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7215-1.5223-2.3877.26471.93286.8991-0.0104-0.2965-0.32560.7349-0.07950.39370.33140.16360.0780.4741-0.0085-0.07120.30780.07170.3042-20.476415.676214.228
25.34380.45811.18742.552-0.49217.89480.342-0.31020.09690.4921-0.07470.3418-0.4773-1.5553-0.15040.4260.04080.030.4560.04570.4043-31.787620.65110.4053
38.8973-2.0038-4.5224.74921.75429.20980.20920.33450.732-0.0470.0739-0.3753-0.89830.3676-0.32710.3647-0.097-0.0610.33680.04490.4016-15.193621.5515-1.222
47.5268-1.1352-1.63265.2252.56286.0246-0.09490.6356-0.2515-0.18930.00960.2888-0.1209-0.33640.07160.282-0.01-0.07160.46140.08480.2875-18.180713.4116-15.1373
52.7078-0.5178-0.60763.28681.76437.165-0.01350.2068-0.12030.09920.1776-0.22030.4520.712-0.20430.27460.0157-0.03630.36620.04720.3365-12.87029.2093-6.1634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 143 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 57 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 143 )

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