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- PDB-8i56: CfbA S11T variant -

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Basic information

Entry
Database: PDB / ID: 8i56
TitleCfbA S11T variant
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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 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)33,1362
Polymers33,1362
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-26 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.060, 67.060, 82.630
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: 16568.070 Da / Num. of mol.: 2 / Mutation: S11T
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.: 7 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
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: BL-1A / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 2, 2022
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 8721 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.048 / Net I/σ(I): 30.32
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.84-2.850.858920.8810.8881
2.85-2.860.7171030.8910.7421
2.86-2.90.8593390.8940.8891
2.9-3.10.47314630.9770.491
3.1-3.30.21911460.9940.2271
3.3-3.50.1379130.9970.1421
3.5-40.07715130.9990.081
4-4.50.0499390.9990.0511
4.5-50.0425840.9990.0441
5-60.0396820.9990.041
6-100.02873810.0291
10-500.02520910.0261

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→47.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 32.299 / SU ML: 0.273 / Cross valid method: FREE R-VALUE / ESU R: 0.929 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25326 436 5 %RANDOM
Rwork0.17072 ---
obs0.17471 8285 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 2.84→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 7 1921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.961.6392657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51420.98102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30815370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7181518
X-RAY DIFFRACTIONr_chiral_restr0.1290.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4437.086964
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.96910.5941199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.9547.532998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.4367733
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3545 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 33 -
Rwork0.377 627 -
obs--100 %
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)
10.6835-0.1369-1.48322.3845-1.92085.30950.1090.25640.0729-0.4286-0.1018-0.21950.1499-0.5134-0.00720.31040.0429-0.13510.1542-0.02250.250117.502815.969-13.0385
21.3621-1.1214-0.25560.99150.23725.86980.0918-0.0672-0.1837-0.2032-0.07990.169-0.19680.7413-0.01190.29410.0558-0.01810.2956-0.05210.198828.486216.5884-12.0642
31.0736-0.087-0.36170.2442-1.14516.15310.0363-0.244-0.17630.1696-0.06030.0355-1.07360.30840.0240.3385-0.0093-0.00560.1461-0.07020.199222.856421.2189-4.8642
41.1881.5478-2.68872.0441-3.55656.19-0.0183-0.1283-0.060.0381-0.0991-0.0913-0.06720.09330.11740.1060.0022-0.00710.4355-0.07420.251319.744911.103312.364
51.79050.0401-1.61720.3934-1.18265.4637-0.0911-0.59430.00670.15170.0547-0.1337-0.38610.26370.03650.11880.0846-0.06950.3473-0.07170.250718.083713.648916.3024
61.1488-0.38851.25480.37540.63195.99310.1706-0.32460.02170.00070.0516-0.05080.6395-0.4602-0.22220.3204-0.076-0.04490.21670.02070.27814.36934.10338.5281
71.8823-1.62471.20471.5597-1.52472.2674-0.2756-0.36750.0102-0.02590.29940.00030.6431-0.1988-0.02380.51680.0104-0.01210.2292-0.00020.018211.9841-4.317417.0722
81.17281.0279-2.89432.0668-2.02177.54680.14060.2551-0.0132-0.1805-0.0684-0.2864-0.4883-0.9728-0.07220.17960.1273-0.04240.39060.0280.21712.563818.0261-0.207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 40
2X-RAY DIFFRACTION2A41 - 83
3X-RAY DIFFRACTION3A84 - 143
4X-RAY DIFFRACTION4B1 - 14
5X-RAY DIFFRACTION5B15 - 58
6X-RAY DIFFRACTION6B59 - 83
7X-RAY DIFFRACTION7B84 - 118
8X-RAY DIFFRACTION8B119 - 143

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