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- PDB-6m2f: Sirohydrochlorin nickelochelatase CfbA in complex with nickel-sir... -

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Basic information

Entry
Database: PDB / ID: 6m2f
TitleSirohydrochlorin nickelochelatase CfbA in complex with nickel-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-sirohydrochlorin / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)34,0283
Polymers33,1082
Non-polymers9201
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-31 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.240, 68.240, 82.010
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-F0L / nickel-sirohydrochlorin


Mass: 919.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44N4NiO16 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.3M Na-malonate, 0.1M Tris, 8% (w/v) gamma-PGA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.48539 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: 1.48539 Å / Relative weight: 1
ReflectionResolution: 2.4→48.25 Å / Num. obs: 14774 / % possible obs: 100 % / Redundancy: 6.854 % / Biso Wilson estimate: 79.866 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.07 / Χ2: 1.039 / Net I/σ(I): 14.81 / Num. measured all: 198167
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
2.4-2.57.150.7332.7123839333433340.7930.791100
2.5-2.67.0770.5013.9920070283628360.9110.542100
2.6-2.77.0830.355.5417255243624360.9580.377100
2.7-2.87.0160.2437.5414712209720970.9820.262100
2.8-2.96.8930.1979.4612615183018300.9820.213100
2.9-36.7520.14411.7410581156715670.9910.156100
3-3.16.3140.10814.338833139913990.9940.118100
3.1-3.26.5550.09816.57990122112190.9930.10699.8
3.2-3.36.340.08518.536708105810580.9940.093100
3.3-3.47.0930.07721.2270089889880.9960.084100
3.4-3.57.070.07522.0356848068040.9970.08199.8
3.5-46.9410.06624.7221463309330920.9970.071100
4-66.5070.05926.2628632440244000.9970.064100
6-106.8970.05528.2310028145514540.9980.0699.9
10-48.256.890.04928.4127494023990.9980.05399.3

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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: 2.4→48.25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 16.888 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2647 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.204 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 739 5 %RANDOM
Rwork0.1895 ---
obs0.1911 14035 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 225 Å2 / Biso mean: 84.743 Å2 / Biso min: 43.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 63 6 1989
Biso mean--159.13 74.01 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122020
X-RAY DIFFRACTIONr_angle_refined_deg2.7321.6922748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23121100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.87115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1471518
X-RAY DIFFRACTIONr_chiral_restr0.1660.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021524
Refine LS restraints NCS

Ens-ID: 1 / Number: 3611 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 54 -
Rwork0.29 1030 -
all-1084 -
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)
11.9195-0.41220.15390.39571.01583.6482-0.09430.4647-0.2629-0.0583-0.08460.1349-0.2680.01210.1790.0292-0.0352-0.01810.22320.03430.1423-17.44113.2004-15.1562
20.07670.10980.42510.34920.15563.64990.07080.05090.0230.1399-0.03770.05910.43960.6229-0.03310.14470.0785-0.01090.134-0.01480.1174-13.56048.8494-4.943
30.2749-0.3365-0.87051.8997-0.0233.6145-0.05-0.0373-0.09710.4596-0.11990.1968-0.08120.23840.16990.2093-0.0289-0.02290.02770.00640.1431-21.034516.834615.4908
45.8281-2.23571.44424.18393.33265.12460.1465-0.418-0.40620.3242-0.19390.16050.301-0.75330.04740.18480.1147-0.10640.3521-0.05210.149-32.375917.93446.5982
51.1379-0.4284-2.03660.54411.83766.9163-0.06160.3717-0.1244-0.1998-0.0704-0.0016-0.6565-0.37250.1320.2096-0.09510.030.1747-0.00890.0823-19.414122.06253.6657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 62
2X-RAY DIFFRACTION2A63 - 143
3X-RAY DIFFRACTION3B1 - 63
4X-RAY DIFFRACTION4B64 - 112
5X-RAY DIFFRACTION5B113 - 143

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