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- PDB-6m27: Sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ -

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Basic information

Entry
Database: PDB / ID: 6m27
TitleSirohydrochlorin nickelochelatase CfbA in complex with Ni2+
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 / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2254
Polymers33,1082
Non-polymers1172
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-45 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.210, 68.210, 81.210
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
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: 1.48644 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: 1.48644 Å / Relative weight: 1
ReflectionResolution: 2.6→41.47 Å / Num. obs: 11541 / % possible obs: 100 % / Redundancy: 9.86 % / Biso Wilson estimate: 73.105 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.089 / Χ2: 1.05 / Net I/σ(I): 18.26 / Num. measured all: 222269
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
2.6-2.79.9570.9893.0624355244624460.7651.045100
2.7-2.89.3310.7793.919380207720770.8420.827100
2.8-2.99.2660.5595.916605179217920.940.593100
2.9-310.1230.3669.2516045158515850.9890.386100
3-3.110.5820.29911.7714677138713870.9930.314100
3.1-3.210.4190.22714.7112513120112010.9940.239100
3.2-3.310.3990.19217.2910690102810280.9940.202100
3.3-3.410.1880.14918.9299439769760.9970.157100
3.4-3.59.9960.14620.3781378148140.9960.154100
3.5-3.69.9180.11522.2477467817810.9960.121100
3.6-3.79.6660.10723.7362836506500.9970.113100
3.7-3.89.3730.08826.0357556146140.9960.093100
3.8-3.98.6740.08824.9945805285280.9970.093100
3.9-48.7060.07827.3441794804800.9970.083100
4-610.0160.06632.943629435643560.9970.069100
6-109.7040.05135.6113935143714360.9990.05499.9
10-41.479.7370.04537.1338173963920.9970.04899

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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: 2.6→41.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2464 / WRfactor Rwork: 0.2081 / FOM work R set: 0.8021 / SU B: 21.681 / SU ML: 0.206 / SU R Cruickshank DPI: 0.3873 / SU Rfree: 0.2545 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 577 5 %RANDOM
Rwork0.192 ---
obs0.1939 10964 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.67 Å2 / Biso mean: 69.405 Å2 / Biso min: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 2.6→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 2 11 1917
Biso mean--84.16 55.74 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121938
X-RAY DIFFRACTIONr_angle_refined_deg2.4321.6382614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85821100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.26115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3271518
X-RAY DIFFRACTIONr_chiral_restr0.1880.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021440
Refine LS restraints NCS

Ens-ID: 1 / Number: 3608 / 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: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 42 -
Rwork0.348 811 -
all-853 -
obs--100 %
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)
112.535-1.5832-7.29443.93060.630410.8999-0.6699-0.2207-0.7578-0.07270.18540.11980.30120.04870.48450.1193-0.0411-0.00650.04090.04230.0735-20.713712.1974-11.0873
26.48820.3692-1.32947.2052.3523.9107-0.06710.6935-0.0972-0.4401-0.01170.1411-0.2154-0.30840.07880.1093-0.0281-0.05030.24350.06090.0489-17.758513.8354-15.7884
31.9822-0.75470.82111.9705-0.72529.1588-0.02850.3153-0.483-0.19740.17240.11691.00450.007-0.14380.1515-0.02790.02560.1629-0.04110.1628-14.14993.773-8.8089
42.4287-2.3266-1.30328.53778.63279.52680.560.926-0.6191-0.0748-0.48020.07260.6012-0.1226-0.07981.1399-0.1131-0.05110.6328-0.12340.5893-10.1301-2.0911-16.4247
55.6664-3.5834-4.12586.40974.94318.9319-0.1196-0.38360.37480.39960.2575-0.0884-0.43480.7488-0.13790.1387-0.0694-0.01560.09270.00870.0698-13.867921.8983.7113
62.5321-1.1923-0.22355.74282.86364.86750.1288-0.0213-0.0959-0.2293-0.44880.3249-0.099-0.24350.32010.0811-0.0301-0.01820.12260.03150.0786-21.910913.424311.2868
77.5820.5661-3.05727.01561.25864.69890.0015-0.5578-0.19860.6554-0.09730.1240.32280.17150.09580.2101-0.0098-0.0510.10950.04310.049-20.244816.364216.0262
81.7441-0.39030.89562.47430.09929.37640.3094-0.2487-0.03210.3716-0.08250.456-0.1253-1.0709-0.22690.1761-0.02920.05210.141-0.00020.1391-29.981219.90069.1034
911.19243.43777.16951.98010.17869.03130.2211-0.3961-0.06120.0268-0.156-0.00540.2676-0.2209-0.06510.43440.0413-0.01130.3629-0.06360.3694-40.466519.361114.8578
108.7737-2.3704-5.49984.04522.27339.68750.43910.15060.1171-0.0637-0.1512-0.0757-1.0120.0418-0.2880.1641-0.0505-0.02590.03750.04010.0742-17.841922.12931.849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 57
3X-RAY DIFFRACTION3A58 - 87
4X-RAY DIFFRACTION4A88 - 122
5X-RAY DIFFRACTION5A123 - 143
6X-RAY DIFFRACTION6B1 - 15
7X-RAY DIFFRACTION7B16 - 57
8X-RAY DIFFRACTION8B58 - 86
9X-RAY DIFFRACTION9B87 - 115
10X-RAY DIFFRACTION10B116 - 143

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