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- PDB-5zt8: SirB from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5zt8
TitleSirB from Bacillus subtilis
ComponentsSirohydrochlorin ferrochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homology: / sirohydrochlorin 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 / MOLECULAR REPLACEMENT / Resolution: 2 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 22, 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 ferrochelatase
B: Sirohydrochlorin ferrochelatase


Theoretical massNumber of molelcules
Total (without water)60,4752
Polymers60,4752
Non-polymers00
Water5,477304
1
A: Sirohydrochlorin ferrochelatase


Theoretical massNumber of molelcules
Total (without water)30,2381
Polymers30,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sirohydrochlorin ferrochelatase


Theoretical massNumber of molelcules
Total (without water)30,2381
Polymers30,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.690, 53.370, 80.430
Angle α, β, γ (deg.)90.000, 105.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 253)
21(chain B and resid 1 through 253)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 253 / Label seq-ID: 13 - 265

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 253)AA
2(chain B and resid 1 through 253)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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2016
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.766 Å / Num. obs: 38718 / % possible obs: 99.3 % / Redundancy: 3.448 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.08 / Χ2: 1.104 / Net I/σ(I): 14.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.13.3070.6691.93101740.7410.79998.9
2.1-2.23.6110.4692.8984490.8130.55399.7
2.2-2.33.5420.3453.9570800.9110.40899.3
2.3-2.43.5610.2665.0559000.9310.31499.7
2.4-2.53.5420.2186.1550190.9560.25799.7
2.5-33.3140.1210.32162140.9870.14399.5
3-3.53.5660.05123.7482810.9970.0699.6
3.5-43.4640.03335.1846070.9980.03999.1
4-63.2460.02342.7465440.9990.02898.6
6-103.7270.01951.2821900.9990.02399.4
10-38.7663.6340.01461.2357910.01796.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZT7

5zt7


Resolution: 2→38.766 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.38
RfactorNum. reflection% reflection
Rfree0.2183 1936 5 %
Rwork0.1852 --
obs0.1868 38693 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.25 Å2 / Biso mean: 38.002 Å2 / Biso min: 17.27 Å2
Refinement stepCycle: final / Resolution: 2→38.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 0 304 4292
Biso mean---44.75 -
Num. residues----511
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1534X-RAY DIFFRACTION8.854TORSIONAL
12B1534X-RAY DIFFRACTION8.854TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.3071380.265426282766100
2.05-2.10550.30591340.25532539267399
2.1055-2.16740.26941380.223926232761100
2.1674-2.23740.25141380.213726232761100
2.2374-2.31730.25291380.21622604274299
2.3173-2.41010.27471370.206326072744100
2.4101-2.51970.26691380.200326302768100
2.5197-2.65260.21581380.204626172755100
2.6526-2.81870.24631380.207626102748100
2.8187-3.03630.23431390.199326432782100
3.0363-3.34170.24051390.189526382777100
3.3417-3.82480.18551390.164826432782100
3.8248-4.81750.17781390.147626442783100
4.8175-38.77370.18441430.16982708285199
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)
12.20550.52380.45033.2183-0.06921.4612-0.01490.09970.0843-0.09520.10780.0292-0.00720.1377-0.10430.2717-0.02670.04240.24960.0040.1376-10.20723.823225.37
23.40920.75681.26572.5611-0.47064.0470.1002-0.1464-0.0208-0.01910.1481-0.0512-0.2185-0.1296-0.23980.22710.00530.02760.232-0.01360.2434-16.75731.094930.1787
36.2579-0.12950.08253.4998-0.33162.67310.3977-0.29610.18310.17530.11380.3046-0.3182-0.3785-0.46010.253-0.02070.08070.26850.0230.2546-19.3499-2.976735.8992
43.0814.7563-0.46457.5116-0.70853.83-0.18370.7139-0.918-0.25550.083-0.67590.11170.27740.08760.25320.0580.05740.3081-0.03890.364310.7901-5.047728.2131
56.1629-1.4071-2.62952.75021.88734.663-0.17480.1343-0.27080.37950.0253-0.3160.2463-0.04350.16010.2609-0.0048-0.05010.1888-0.02430.424313.3829-2.101238.4366
63.5855-0.4267-0.61352.77561.39753.70490.2073-0.1804-0.58790.4864-0.1859-0.0560.4992-0.1377-0.03760.3142-0.0578-0.07020.22320.05590.40410.3607-3.394243.4057
71.9517-0.2126-1.44293.99940.73532.3418-0.01210.1957-0.43520.3422-0.0872-0.44420.1050.2090.10880.26760.01-0.0290.18970.01670.427115.67542.670537.5422
82.7677-0.99293.09523.0737-1.07283.427-0.0442-0.3310.7388-0.2781-0.1382-0.4598-0.1644-0.11730.21850.30930.00440.00850.2316-0.04010.424315.286912.187839.6458
93.40512.15190.7531.70150.18451.0657-0.04640.0261-0.494-0.07980.1172-0.32310.1745-0.01-0.05990.22480.0605-0.00320.1905-0.02670.3475-3.0379-5.479231.8602
103.5464-0.76360.44314.9318-0.90333.2607-0.0661-0.04070.36520.05220.1807-0.4674-0.30810.0601-0.09320.2639-0.0549-0.03260.2596-0.04250.211644.516715.827910.9143
113.3244-1.28690.2711.60270.25461.25870.09260.39540.0797-0.336-0.0653-0.2052-0.10290.0606-0.06630.37580.00270.04690.3120.00470.218142.244111.90470.675
122.4963-0.7115-0.10041.751-0.51722.0233-0.1451-0.2336-0.2026-0.16120.35130.29140.2948-0.4249-0.08060.2825-0.0395-0.0020.29940.08170.286516.54719.904315.0365
133.9761-0.5177-1.31873.8804-0.97783.89960.04490.1866-0.2453-0.31940.09440.51750.3009-0.2615-0.15790.3207-0.0806-0.06220.32460.05560.268413.466612.48895.8813
144.4835-0.9801-0.95022.7227-0.13621.6670.2599-0.15210.05050.02050.1230.2904-0.3112-0.4067-0.27180.38860.020.0440.36620.08320.280912.334121.821914.851
156.1524-2.4071-0.04222.46290.0311.2694-0.0476-0.74280.07510.2610.30340.3864-0.0807-0.1676-0.21120.33930.04450.06870.46790.03270.321416.137416.916919.0336
163.3232-1.9966-0.36192.78281.27341.5537-0.0370.1198-0.1055-0.18410.0354-0.00110.3537-0.0213-0.07010.3066-0.0284-0.01660.21640.0120.18838.11433.30366.6188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 79 )A32 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 106 )A80 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 120 )A107 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 138 )A121 - 138
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 180 )A139 - 180
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 198 )A181 - 198
8X-RAY DIFFRACTION8chain 'A' and (resid 199 through 214 )A199 - 214
9X-RAY DIFFRACTION9chain 'A' and (resid 215 through 256 )A215 - 256
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 58 )B-1 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 106 )B59 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 138 )B107 - 138
13X-RAY DIFFRACTION13chain 'B' and (resid 139 through 180 )B139 - 180
14X-RAY DIFFRACTION14chain 'B' and (resid 181 through 214 )B181 - 214
15X-RAY DIFFRACTION15chain 'B' and (resid 215 through 227 )B215 - 227
16X-RAY DIFFRACTION16chain 'B' and (resid 228 through 253 )B228 - 253

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