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- PDB-6m26: Sirohydrochlorin nickelochelatase CfbA in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 6m26
TitleSirohydrochlorin nickelochelatase CfbA in P212121 space group
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
Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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

Downloads & links

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Assembly

Deposited unit
A: Sirohydrochlorin cobaltochelatase
B: Sirohydrochlorin cobaltochelatase


Theoretical massNumber of molelcules
Total (without water)33,1082
Polymers33,1082
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-29 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.430, 64.380, 69.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.2M ammonium formate, 20 % (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: 1.48644 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48644 Å / Relative weight: 1
ReflectionResolution: 2.61→47.17 Å / Num. obs: 9065 / % possible obs: 100 % / Redundancy: 13.139 % / Biso Wilson estimate: 49.815 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.192 / Rrim(I) all: 0.2 / Χ2: 0.989 / Net I/σ(I): 12.78 / Num. measured all: 219102 / Scaling rejects: 16
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
2.61-2.7110.9630.952.3319547178617830.8190.99799.8
2.71-2.8113.5760.7693.5220568151515150.9020.799100
2.81-313.5820.5685.1332693240724070.9540.591100
3-3.512.710.3099.6351566405740570.9860.322100
3.5-413.8720.20217.0931684228422840.9960.209100
4-613.5810.14622.7544260326032590.9970.152100
6-1013.6850.09126.9114698107410740.9980.095100
10-47.1713.7580.06533.9440862972970.9980.067100

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Processing

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

2xws


Resolution: 2.61→47.17 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.99 / SU ML: 0.271 / SU R Cruickshank DPI: 1.0136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.014 / ESU R Free: 0.345 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 454 5 %RANDOM
Rwork0.1957 ---
obs0.1993 8611 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 141.1 Å2 / Biso mean: 45.962 Å2 / Biso min: 21.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 2.61→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 37 2020
Biso mean---37.97 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122014
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.6382720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73821.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.61115386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191518
X-RAY DIFFRACTIONr_chiral_restr0.1430.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021498
Refine LS restraints NCS

Ens-ID: 1 / Number: 3424 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.61→2.678 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 33 -
Rwork0.356 624 -
all-657 -
obs--99.85 %
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)
14.29820.20572.83640.9991-0.23182.0090.08660.06410.18740.0771-0.11870.24940.03680.08590.03210.0646-0.02450.01030.0405-0.02040.0692-12.981117.98571.0172
24.1493-1.13071.94522.8545-1.95131.70880.1837-0.154-0.0209-0.0278-0.1060.13160.06990.0245-0.07770.03440.00150.0090.0870.0080.0112-9.122117.9546.6108
32.024-0.3711-0.3660.1074-0.121.94390.0334-0.11710.0752-0.0053-0.016-0.0093-0.1341-0.0751-0.01740.1111-0.00380.02170.1011-0.02070.0093-9.021528.78023.0311
46.8122-1.9436-2.46131.2280.73960.9409-0.10770.5127-0.02880.08320.09650.0424-0.099-0.15580.01120.4074-0.03160.00060.19410.02720.0294-8.448642.1734-1.8107
51.2267-0.1122-0.6480.40710.84491.95270.0228-0.0130.1247-0.12190.0756-0.0166-0.17680.1656-0.09840.1297-0.0002-0.02870.0182-0.00980.024-3.179820.6727-2.1674
60.0961-0.194-0.33334.00892.69292.28670.02140.053-0.0334-0.0414-0.0873-0.0288-0.0674-0.16080.06590.10980.05950.00010.07830.00180.0253-6.946717.4783-20.1037
72.0669-1.15240.17043.61981.18230.5658-0.01230.04150.0208-0.12420.0711-0.1603-0.07650.0478-0.05880.1153-0.01190.00750.02320.01010.0186-0.928314.6449-20.9167
80.2837-0.62290.07481.56740.50452.38830.0340.05370.0141-0.096-0.16040.0103-0.1285-0.05380.12640.0963-0.00010.00290.0754-0.01660.0113-9.544311.1313-24.4352
94.41280.0948-0.90333.78934.81826.36470.24220.2374-0.1606-0.1273-0.54330.2047-0.2245-0.7490.30110.09160.0485-0.0230.1267-0.01780.0345-20.608510.0336-20.1284
105.0429-3.09830.10761.9065-0.06030.12160.15740.6245-0.3174-0.0857-0.38170.20690.0101-0.00270.22430.0610.01230.00540.0931-0.06930.4648-20.236910.6816-31.4866
110.4988-0.308-0.06580.26590.28322.19280.0268-0.0766-0.01180.10050.02490.01740.3681-0.1048-0.05170.1832-0.03330.00690.0324-0.00990.0168-3.821610.8126-7.9373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 45
3X-RAY DIFFRACTION3A46 - 85
4X-RAY DIFFRACTION4A86 - 90
5X-RAY DIFFRACTION5A110 - 143
6X-RAY DIFFRACTION6B1 - 15
7X-RAY DIFFRACTION7B16 - 43
8X-RAY DIFFRACTION8B44 - 74
9X-RAY DIFFRACTION9B75 - 88
10X-RAY DIFFRACTION10B89 - 116
11X-RAY DIFFRACTION11B117 - 143

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