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- PDB-5zt9: SirB from Bacillus subtilis with Ni2+ -

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Basic information

Entry
Database: PDB / ID: 5zt9
TitleSirB from Bacillus subtilis with Ni2+
ComponentsSirohydrochlorin ferrochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homologysirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / Sirohydrochlorin cobaltochelatase CbiX-like / CbiX / siroheme biosynthetic process / metal ion binding / NICKEL (II) ION / Sirohydrochlorin ferrochelatase
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / 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)60,7106
Polymers60,4752
Non-polymers2354
Water1,11762
1
A: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3553
Polymers30,2381
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sirohydrochlorin ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3553
Polymers30,2381
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.730, 53.700, 78.020
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 254)
21(chain B and resid 2 through 254)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 254 / Label seq-ID: 14 - 266

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 2 through 254)AA
2(chain B and resid 2 through 254)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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, 20 %(w/v) PEG 6000, 10mM Nickel sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2017
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: 2.8→43.426 Å / Num. obs: 13781 / % possible obs: 99.4 % / Redundancy: 3.487 % / Biso Wilson estimate: 51.61 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.21 / Χ2: 0.914 / Net I/σ(I): 6.24 / Num. measured all: 92210 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.93.4230.9971.2726490.5121.18599.6
2.9-33.4690.7651.723010.6350.90799.3
3-3.13.6640.6072.219860.7480.71199.5
3.1-3.23.630.4842.7317960.8310.56999.8
3.2-3.33.6180.4043.2315720.8640.47599.4
3.3-3.53.5780.3174.0526370.9150.37399.7
3.5-43.3880.1776.7244620.9620.2199.2
4-4.53.2620.119.8326880.9820.13299.8
4.5-63.6190.10510.4436830.9870.12399.2
6-103.2960.07112.8821030.9940.08599.1
10-43.4263.6910.05518.835670.9960.06497.8

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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: 2.8→43.426 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2453 690 5.01 %
Rwork0.2119 --
obs0.2137 13777 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.33 Å2 / Biso mean: 56.7861 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: final / Resolution: 2.8→43.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 4 62 4043
Biso mean--77.3 40.28 -
Num. residues----510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2426X-RAY DIFFRACTION9.595TORSIONAL
12B2426X-RAY DIFFRACTION9.595TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8001-3.01620.29311380.264626072745
3.0162-3.31960.29581350.254125792714
3.3196-3.79970.27571380.224826082746
3.7997-4.78630.23661370.190926062743
4.7863-43.43120.19921420.189326872829
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)
14.27630.63891.02221.55931.23864.030.05760.55440.3458-0.13750.15130.1055-0.0970.0573-0.22290.37920.02480.00970.37310.11540.3085-10.80085.090324.53
24.3912-0.13871.84322.6953-1.33572.20910.0548-0.6051-0.43490.27090.16940.4116-0.1027-0.3997-0.24860.3227-0.04380.00920.40390.11890.3331-18.82950.906231.6654
34.28171.13471.51143.1920.1662.45260.2997-0.2074-0.54940.1542-0.1716-0.23550.3151-0.0709-0.13210.36860.0056-0.05110.22350.07180.39758.5846-4.639635.418
43.20731.17240.83484.55250.72262.62480.0576-0.6581-0.2260.32930.0704-0.35730.1043-0.0324-0.12460.33180.0371-0.02740.31830.03770.381213.3632.256940.6685
55.68051.51111.00052.39730.0811.20390.4994-0.3795-0.43680.1741-0.2316-0.0244-0.0227-0.1312-0.20640.39090.0088-00.28620.01580.37280.71910.473533.2002
64.10050.9646-0.19314.2397-1.05412.87890.11790.46080.0892-0.08220.0846-0.283-0.24330.1737-0.18570.38540.03170.04090.3854-0.0190.257442.257214.49895.2311
75.0443-0.2806-2.03484.5484-1.07963.5477-0.14270.85030.4735-0.70340.22490.27490.3535-0.534-0.11760.5063-0.0378-0.04160.52450.11980.477316.43697.84899.6264
82.3943-1.2771.58996.6833-0.7442.32470.09541.02210.6729-0.28480.2040.0574-0.221-0.2601-0.32050.5601-0.0729-0.08971.02430.33940.76859.62815.6094.6639
95.24870.7654-1.46681.5825-1.29483.89270.2460.05190.36010.03730.21810.713-0.3641-0.497-0.4430.36560.011-0.00330.42620.06120.465421.087413.860410.7441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 106 )A32 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 155 )A107 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 198 )A156 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 257 )A199 - 257
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 106 )B1 - 106
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 155 )B107 - 155
8X-RAY DIFFRACTION8chain 'B' and (resid 156 through 180 )B156 - 180
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 254 )B181 - 254

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