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- PDB-5zt7: SirB from Bacillus subtilis with Co2+ -

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Basic information

Entry
Database: PDB / ID: 5zt7
TitleSirB from Bacillus subtilis with Co2+
ComponentsSirohydrochlorin ferrochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homologysirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / Sirohydrochlorin cobaltochelatase CbiX-like / CbiX / siroheme biosynthetic process / metal ion binding / : / Sirohydrochlorin ferrochelatase
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.94 Å
AuthorsFujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
CitationJournal: Dalton Trans / Year: 2019
Title: Structure of sirohydrochlorin ferrochelatase SirB: the last of the structures of the class II chelatase family.
Authors: Fujishiro, T. / Shimada, Y. / Nakamura, R. / Ooi, M.
History
DepositionMay 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Mar 4, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 ferrochelatase
B: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,00511
Polymers60,4752
Non-polymers5309
Water55831
1
A: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4735
Polymers30,2381
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5326
Polymers30,2381
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.960, 52.090, 75.470
Angle α, β, γ (deg.)90.000, 112.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 251)
21(chain B and resid 2 through 251)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 2 - 251 / Label seq-ID: 14 - 263

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 2 through 251)AA
2(chain B and resid 2 through 251)BB

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Components

#1: Protein Sirohydrochlorin ferrochelatase /


Mass: 30237.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sirB, ylnE, BSU15620 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: O34632, sirohydrochlorin ferrochelatase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.1 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Lithium acetate, 20% (w/v) PEG 3350, 10 mM Cobalt chlroide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.0, 1.60518, 1.60612, 1.56556
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2016
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator,
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.605181
31.606121
41.565561
ReflectionResolution: 2.94→36.845 Å / Num. obs: 10156 / % possible obs: 99.3 % / Redundancy: 3.427 % / Biso Wilson estimate: 83.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.118 / Χ2: 0.991 / Net I/σ(I): 9.14 / Num. measured all: 66619 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.94-3.043.4760.9441.2818820.6031.11999.2
3.04-3.053.4970.8121.611850.6440.961100
3.05-3.33.4190.52.3836170.8650.59399.5
3.3-3.43.1780.3423.2412240.930.41299.1
3.4-3.53.230.254.5510310.9660.30298.9
3.5-43.5340.1577.2738020.9840.18699.3
4-63.4130.07314.0354230.9940.08799.5
6-103.4530.04222.1117930.9970.0599.3
10-36.8453.5690.03729.94800.9970.04495.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.94→36.845 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 506 4.98 %
Rwork0.2457 9648 -
obs0.2472 10154 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.82 Å2 / Biso mean: 88.7062 Å2 / Biso min: 49.24 Å2
Refinement stepCycle: final / Resolution: 2.94→36.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 9 31 3990
Biso mean--106.52 80.37 -
Num. residues----506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2372X-RAY DIFFRACTION8.387TORSIONAL
12B2372X-RAY DIFFRACTION8.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.94-3.23570.34711260.324523922518
3.2357-3.70360.35281240.294723832507
3.7036-4.66460.27111270.246424142541
4.6646-36.84830.23771290.212724592588

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