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- PDB-8iyu: CfbA S11T variant with Ni(II) ions -

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Basic information

Entry
Database: PDB / ID: 8iyu
TitleCfbA S11T variant with Ni(II) ions
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
NICKEL (II) ION / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2544
Polymers33,1362
Non-polymers1172
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-42 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.180, 67.180, 84.110
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


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
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 57.05 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 1.49 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 25, 2023
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21846 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.049 / Net I/σ(I): 20.71
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.20.65328040.8520.71
2.2-2.30.43623730.9190.4671
2.3-2.50.24936730.9740.2681
2.5-2.70.14826630.9890.161
2.7-30.08627800.9970.0921
3-3.50.04727840.9990.051
3.5-40.03715560.9990.0391
4-50.03315510.9990.0361
5-60.0327000.9990.0341
6-100.0317460.9990.0341
10-500.0272160.9990.031

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 1092 5 %
Rwork0.1856 --
obs0.1865 21839 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 2 53 1952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121927
X-RAY DIFFRACTIONf_angle_d1.242605
X-RAY DIFFRACTIONf_dihedral_angle_d38.911259
X-RAY DIFFRACTIONf_chiral_restr0.073311
X-RAY DIFFRACTIONf_plane_restr0.007333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.23261360.21382578X-RAY DIFFRACTION100
2.2-2.310.27561360.21522580X-RAY DIFFRACTION100
2.31-2.460.30411350.21612576X-RAY DIFFRACTION100
2.46-2.650.25111370.22062587X-RAY DIFFRACTION100
2.65-2.910.2751360.24222596X-RAY DIFFRACTION100
2.91-3.330.25351360.21612582X-RAY DIFFRACTION100
3.33-4.20.17121380.16672620X-RAY DIFFRACTION100
4.2-47.50.16531380.15862628X-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)
12.9385-2.0453-2.37234.79013.26075.92660.16170.1526-0.1782-0.0589-0.3060.533-0.0455-0.28870.06340.5612-0.0223-0.05350.43460.03520.4525-22.506914.438411.4927
22.9724-0.1397-3.07327.07660.76294.94130.0033-0.2999-0.06370.55150.0576-0.34420.32960.4836-0.10750.5256-0.0275-0.12940.48250.02160.4044-15.073717.333413.7685
36.75780.68430.45322.27152.45552.68580.0346-0.4966-0.73631.0179-0.11180.68641.0161-0.98060.08750.8033-0.08320.02520.47220.12050.6044-27.563912.807617.1684
42.09830.67561.4973.31541.89259.0680.2052-0.16010.27060.4118-0.25070.3996-0.218-1.36840.06490.52540.01640.03330.5760.02040.5141-31.930220.453410.9423
54.3995-1.2578-2.64352.39081.06688.13120.29970.16260.6924-0.10570.1921-0.4427-0.88830.5725-0.46330.4528-0.0999-0.01460.3881-0.0120.5027-15.26621.2135-1.1562
63.0521-3.4614-2.33553.88662.94736.2406-0.1771-1.144-0.25980.22610.13330.27730.42570.58320.05410.40230.0037-0.02680.50330.04370.4575-18.327610.6866-12.5803
76.98250.0437-1.95043.30332.27015.12370.18970.45640.327-0.3499-0.01380.2414-0.6768-0.2953-0.22470.4501-0.0184-0.02320.47150.10330.3772-16.6218.4827-14.6108
88.3854-0.7628-1.66565.99961.14825.73710.09561.2506-0.4428-0.22050.12470.6940.5253-1.1466-0.0140.4317-0.055-0.11940.6205-0.00650.5551-20.76446.0135-18.142
92.22480.62960.05371.96970.76867.13220.01870.199-0.26430.21790.1211-0.19540.56840.5094-0.10930.42130.0436-0.03910.4897-0.00150.5254-13.15226.0678-9.2021
107.19611.5283-2.01557.05010.1139.3442-0.3240.3151-0.6359-0.37090.4352-0.28122.1421-0.1216-0.33010.8888-0.029-0.07420.5291-0.08490.5404-13.4552-3.3144-13.3728
112.384-0.8884-1.89613.84882.79056.62220.337-0.11060.4931-0.23850.1976-0.6613-0.68870.7373-0.47770.4663-0.0878-0.00090.4854-0.00060.4894-12.391218.32740.2173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 40 )
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 78 )
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 143 )

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