[English] 日本語
Yorodumi
- PDB-5zt9: SirB from Bacillus subtilis with Ni2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zt9
TitleSirB from Bacillus subtilis with Ni2+
ComponentsSirohydrochlorin ferrochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homology: / sirohydrochlorin 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more