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- PDB-8i57: Uroporphyrin III (UPIII)-bound CfbA -

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Basic information

Entry
Database: PDB / ID: 8i57
TitleUroporphyrin III (UPIII)-bound CfbA
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
Chem-UP3 / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 / _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)33,9393
Polymers33,1082
Non-polymers8311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-31 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.220, 68.220, 82.650
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 (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: Chemical ChemComp-UP3 / 3,3',3'',3'''-[3,8,13,17-tetrakis(carboxymethyl)porphyrin-2,7,12,18-tetrayl]tetrapropanoic acid


Mass: 830.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H38N4O16 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.9 Å3/Da / Density % sol: 57.65 %
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-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 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: 2.81→50 Å / Num. obs: 9294 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.046 / Net I/σ(I): 23.62
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.81-2.910.959090.5671.0741
2.91-3.040.57910280.7840.6551
3.04-3.20.33410400.9170.3791
3.2-3.40.17910500.970.2041
3.4-3.60.1098190.990.1241
3.6-40.06311950.9960.0721
4-4.50.0349530.9990.0391
4.5-50.0256150.9990.0281
5-60.0267050.9990.0291
6-100.01676310.0181
10-500.01321710.0151

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→35.35 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 465 5.01 %
Rwork0.2071 --
obs0.2087 9285 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 60 0 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161989
X-RAY DIFFRACTIONf_angle_d2.7352694
X-RAY DIFFRACTIONf_dihedral_angle_d7.177287
X-RAY DIFFRACTIONf_chiral_restr0.191311
X-RAY DIFFRACTIONf_plane_restr0.021344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.220.35371540.3092919X-RAY DIFFRACTION100
3.22-4.050.30041540.2342923X-RAY DIFFRACTION100
4.05-35.350.18871570.17842978X-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)
10.1384-0.30011.0550.0737-0.15870.2750.7901-0.16210.2723-0.4414-1.32650.17810.0473-0.5423-00.93240.0299-0.04490.6773-0.06030.594311.510719.1927-11.4186
20.4577-0.03790.38280.7403-0.67461.91840.10730.16710.2284-0.5663-0.06580.1116-0.34940.3878-00.7160.09540.00470.54640.04970.688714.076517.796-15.1794
3-0.5626-0.65520.18370.1415-0.36032.7350.1325-0.38320.0478-0.2558-0.0545-0.16260.5743-0.504600.5934-0.01320.00270.55190.05490.51158.913713.0064-5.3303
41.35940.2702-1.28540.85542.23974.018-0.0393-0.54310.2347-0.13490.17460.3004-0.1338-0.006900.46080.05580.01510.6130.01450.558817.033823.277113.4141
5-0.0013-0.0151-0.0122-0.05810.24360.03980.25370.24322.2583-0.03212.19880.69160.25580.3367-01.1049-0.07450.14170.883-0.5430.57621.879836.887118.2113
60.0991-0.02890.72930.0074-0.61740.75790.1478-0.2993-0.083-0.0603-0.1418-0.10640.22050.561500.594-0.00690.05960.5927-0.0010.592221.564415.3853-0.1903
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 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 143 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 143 )

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