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- PDB-6m29: Sirohydrochlorin nickelochelatase CfbA in complex with Co2+ and f... -

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Basic information

Entry
Database: PDB / ID: 6m29
TitleSirohydrochlorin nickelochelatase CfbA in complex with Co2+ and formate
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
: / FORMIC ACID / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2725
Polymers33,1082
Non-polymers1643
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-52 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 82.470
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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 57.52 %
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: 1.60581 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 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: 1.60581 Å / Relative weight: 1
ReflectionResolution: 2.9→48.34 Å / Num. obs: 8427 / % possible obs: 99.2 % / Redundancy: 4.334 % / Biso Wilson estimate: 86.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.084 / Χ2: 1.04 / Net I/σ(I): 11.13 / Num. measured all: 36522 / Scaling rejects: 114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-34.5430.931.3437398238230.6581.053100
3-3.14.6770.6661.9733217107100.80.752100
3.1-3.24.6430.4452.9228606176160.8920.50399.8
3.2-3.34.4920.4053.8324845555530.8820.46199.6
3.3-3.44.470.2774.7822265014980.9450.31599.4
3.4-3.53.7940.2865.6815294204030.9370.33596
3.5-44.1350.139.736475160115660.9890.1597.8
4-64.2440.05918.889673228522790.9960.06799.7
6-104.3960.04124.5133547647630.9980.04799.9
10-48.343.9860.03426.478612212160.9960.0497.7

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Processing

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

2xws


Resolution: 2.9→48.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2482 / WRfactor Rwork: 0.1918 / FOM work R set: 0.7406 / SU B: 17.606 / SU ML: 0.309 / SU R Cruickshank DPI: 1.7334 / SU Rfree: 0.3549 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.733 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 422 5 %RANDOM
Rwork0.1975 ---
obs0.1998 8005 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 216.03 Å2 / Biso mean: 90.621 Å2 / Biso min: 44.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.9→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 5 3 1946
Biso mean--162.55 68.08 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121976
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6382659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96921100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.41315378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1241518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021456
Refine LS restraints NCS

Ens-ID: 1 / Number: 3724 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 32 -
Rwork0.401 599 -
all-631 -
obs--100 %

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