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- PDB-6m2h: A reaction intermediate of sirohydrochlorin nickelochelatase CfbA... -

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Basic information

Entry
Database: PDB / ID: 6m2h
TitleA reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ and sirohydrochlorin
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
NICKEL (II) ION / Chem-SHN / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 27, 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)34,0885
Polymers33,1082
Non-polymers9803
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-42 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.880, 68.880, 83.000
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SHN / 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid


Mass: 862.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M ammonium sulfate, 0.3M Na-formate, 0.1M Na-acetate, 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: SPring-8 / Beamline: BL44XU / Wavelength: 1.485766 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2019
RadiationMonochromator: liquid-nitrogen-cooled Si(111) double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.485766 Å / Relative weight: 1
ReflectionResolution: 3.1→48.71 Å / Num. obs: 7105 / % possible obs: 99.7 % / Redundancy: 12.831 % / Biso Wilson estimate: 92.576 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.122 / Χ2: 0.929 / Net I/σ(I): 16.3 / Num. measured all: 91166 / Scaling rejects: 186
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
3.1-3.213.7610.9313.0189866536530.830.967100
3.2-3.313.4350.7094.3476045665660.890.738100
3.3-3.412.7070.5585.5262394914910.9450.583100
3.4-3.511.450.636651414574490.9610.66898.2
3.5-412.7570.25411.7820538162016100.990.26699.4
4-612.9570.12123.4630216233223320.9960.126100
6-1012.6330.07231.3398797827820.9980.075100
10-48.7111.5450.06135.2325632242220.9970.06499.1

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Processing

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

2xws


Resolution: 3.1→48.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.1749 / FOM work R set: 0.8291 / SU B: 15.968 / SU ML: 0.284 / SU Rfree: 0.3725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 356 5 %RANDOM
Rwork0.1708 ---
obs0.1732 6748 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 252.73 Å2 / Biso mean: 97.846 Å2 / Biso min: 47.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 3.1→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 64 0 1952
Biso mean--189.61 --
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121989
X-RAY DIFFRACTIONr_angle_refined_deg1.971.6872690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92520.81698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.99715364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7421518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021494
Refine LS restraints NCS

Ens-ID: 1 / Number: 3566 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 27 -
Rwork0.206 499 -
all-526 -
obs--100 %

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