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- PDB-5zta: SirB from Bacillus subtilis with Fe3+ -

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Basic information

Entry
Database: PDB / ID: 5zta
TitleSirB from Bacillus subtilis with Fe3+
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 subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsFujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
CitationJournal: To be published
Title: A route for metal acquisition for chelatase reaction catalyzed by SirB from Bacillus subtilis
Authors: Fujishiro, T.
History
DepositionMay 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5874
Polymers60,4752
Non-polymers1122
Water23413
1
A: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2932
Polymers30,2381
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2932
Polymers30,2381
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.460, 53.430, 79.860
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 252 or resid 301))
21(chain B and (resid 2 through 252 or resid 301))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 252 or resid 301))A0
211(chain B and (resid 2 through 252 or resid 301))B0

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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 subsp. subtilis str. 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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Li-acetate, 20% w/v PEG 3350, 10 mM ammonium ferrous sulfate (air-oxidzed to Fe3+)

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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: 3.07→44.754 Å / Num. obs: 20500 / % possible obs: 99.1 % / Redundancy: 3.332 % / Biso Wilson estimate: 57.58 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.231 / Rrim(I) all: 0.275 / Χ2: 0.771 / Net I/σ(I): 4.02 / Num. measured all: 68297 / Scaling rejects: 59
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
3.07-3.173.4070.951.436493192419060.6611.12799.1
3.17-3.273.2940.7991.65416165616440.7240.95699.3
3.27-3.373.0990.6611.84558148114710.7820.80399.3
3.37-3.473.1750.5582.294093130312890.860.67498.9
3.47-3.573.2060.4472.593738116711660.8630.53899.9
3.57-43.4680.2933.613202383038070.9510.34899.4
4-63.3280.1795.1221578655164840.9740.21399
6-103.3470.1257.167207218021530.9790.14998.8
10-44.7543.4690.10710.4820125895800.9730.12798.5

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Processing

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

5zt7


Resolution: 3.07→44.754 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1019 4.98 %
Rwork0.2346 19459 -
obs0.2362 20478 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.08 Å2 / Biso mean: 70.2023 Å2 / Biso min: 21.32 Å2
Refinement stepCycle: final / Resolution: 3.07→44.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 2 13 3967
Biso mean--84.67 45.78 -
Num. residues----506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2329X-RAY DIFFRACTION10.132TORSIONAL
12B2329X-RAY DIFFRACTION10.132TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0703-3.23220.35481470.346627912938
3.2322-3.43460.35051470.306827822929
3.4346-3.69970.2821480.28427592907
3.6997-4.07180.30661470.231628092956
4.0718-4.66040.25291400.211227572897
4.6604-5.86950.23521440.212328002944
5.8695-44.75920.19811460.179427612907
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)
10.19280.0723-0.10994.0837-0.25382.504-0.1649-0.1845-0.0111-0.95210.0784-0.2832-0.152-0.2028-0.01280.3659-0.0519-0.0090.5519-0.01170.3943-48.4102-3.701928.825
29.61674.9667-0.09537.3372-0.80914.62530.36440.61691.84970.69820.27691.33590.1177-0.0975-0.50050.44830.09190.01930.38690.05180.4072-49.157-1.696925.3117
33.59561.38560.63483.1392-0.16352.42750.2869-0.0715-0.2053-0.26110.215-0.5043-0.3083-0.0393-0.56580.3945-0.07990.10280.4245-0.00070.7046-48.8501-8.875534.0539
46.1910.54550.29241.3285-0.99041.79580.42250.2229-0.10780.09620.028-0.0253-0.178-0.2473-0.45630.4939-0.00380.13210.3546-0.0450.8332-37.1396-9.512334.4062
53.77830.3983-0.28793.52691.02083.44170.1705-0.1243-0.63020.3366-0.2586-0.26290.2231-0.1369-0.00730.5392-0.0010.12460.3530.10310.9115-22.9063-7.860941.4645
63.13520.5741.49441.3141-0.37820.708-0.0282-0.0042-0.23650.376-0.0997-0.020.1232-0.07060.11990.6091-0.020.35090.4321-0.11181.2202-32.1019-6.470533.4728
74.3828-3.71510.00072.1710.97843.452-0.198-1.06070.0838-0.59581.32461.3593-0.21080.1951-1.08430.5256-0.21410.27750.5576-0.18761.26048.37838.49538.8089
86.9179-1.3095-2.38224.73451.59915.08860.3604-0.36661.6819-0.27770.628-1.0587-0.54320.4672-0.99570.4991-0.0940.08530.5107-0.12630.58189.434410.822412.1785
94.2376-2.65370.86644.33380.11491.86440.57820.7210.3099-0.4612-0.42370.3072-0.19860.0806-0.25940.56780.07430.26140.4981-0.03940.93195.10245.77183.0799
102.8443-0.62341.05162.13020.11782.43080.3927-0.56070.8354-0.253-0.2192-0.4297-0.15030.8223-0.21640.68690.09780.35190.64560.01170.77349.15296.0249-0.7863
111.3408-1.0331-0.75192.80390.71643.4815-0.0798-0.07950.22390.24590.63051.95680.5714-0.6344-0.18710.4317-0.14140.17130.56380.18561.1326-18.45573.645514.8362
123.51390.13980.372.9408-0.57093.92720.102-0.195-0.74340.18630.3841.16250.4525-0.8293-0.44580.7121-0.14350.16460.62550.11070.9941-21.42366.36495.5391
133.7763-1.98041.43744.7148-1.43063.75590.1032-0.33650.00710.19650.55160.5884-0.5951-1.1361-0.64330.68650.10030.24120.73760.14350.6525-22.659615.59314.6767
142.0062-6.96512.26044.3993-0.38580.9128-0.951-1.98241.20490.63050.948-0.12-0.5772-0.61380.13380.71260.1210.00510.80920.06740.6221-18.977310.675318.8405
154.6418-1.17540.37627.42285.17213.5071-0.1839-0.0116-0.42730.04430.48640.07720.47960.3359-0.15030.435-0.0296-0.02930.36670.07720.49422.9892-2.83086.9198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )A2 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 58 )A15 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 79 )A59 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 138 )A80 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 198 )A139 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 255 )A199 - 255
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 14 )B1 - 14
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 58 )B15 - 58
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 79 )B59 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 106 )B80 - 106
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 138 )B107 - 138
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 180 )B139 - 180
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 214 )B181 - 214
14X-RAY DIFFRACTION14chain 'B' and (resid 215 through 227 )B215 - 227
15X-RAY DIFFRACTION15chain 'B' and (resid 228 through 252 )B228 - 252

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