[English] 日本語
Yorodumi
- PDB-3h1s: Crystal structure of superoxide dismutase from Francisella tulare... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h1s
TitleCrystal structure of superoxide dismutase from Francisella tularensis subsp. tularensis SCHU S4
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / sobD / superoxide dismutase / CSGID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNocek, B. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of superoxide dismutase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Nocek, B. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionApr 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8577
Polymers44,4692
Non-polymers3885
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.787, 136.787, 59.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

-
Components

#1: Protein Superoxide dismutase


Mass: 22234.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: sodB, FTT0068 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q5NIJ9, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 potassium acetate 20% Peg 3350 0.1 M Cesium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 32840 / Num. obs: 32413 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 38
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3 / Num. unique all: 1617 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ISC
Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.001 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.141 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20502 1647 5.1 %RANDOM
Rwork0.16485 ---
all0.167 32408 --
obs0.1669 30761 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.936 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0.83 Å20 Å2
2---1.66 Å20 Å2
3---2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 20 252 3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223193
X-RAY DIFFRACTIONr_bond_other_d0.0010.022086
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9194340
X-RAY DIFFRACTIONr_angle_other_deg0.93535095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10525.28161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77915512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.136156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.51900
X-RAY DIFFRACTIONr_mcbond_other0.2691.5770
X-RAY DIFFRACTIONr_mcangle_it1.38123068
X-RAY DIFFRACTIONr_scbond_it2.18831293
X-RAY DIFFRACTIONr_scangle_it3.2914.51272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 124 -
Rwork0.229 2205 -
obs--96.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.9579-0.239-0.79313.34260.90186.59290.18770.83470.0214-0.0267-0.24880.85340.0852-0.79970.06110.12880.1158-0.07720.5359-0.06040.67156.715417.3256-2.2622
29.1307-0.67410.86347.1052-4.12892.4335-0.42990.0840.26940.39280.3342-0.0825-0.2843-0.23020.09580.25580.18590.0470.2186-0.06750.658911.137730.05398.7147
33.0453-0.3587-2.41392.25810.72314.01970.1190.38810.1507-0.1136-0.04290.5903-0.399-0.3352-0.07610.21680.078-0.00590.20890.00080.4416.754627.53722.3379
44.0782-1.89461.14955.48162.02263.4719-0.08070.8005-0.4864-0.5279-0.02720.7239-0.48480.06040.10790.16080.0966-0.07010.4568-0.08510.456516.598717.9135-4.2834
58.75412.47562.01196.59550.75664.27060.06510.6384-0.4931-0.7968-0.0860.30580.078-0.38780.02090.2266-0.0058-0.18090.4305-0.20970.442114.6035.4959-11.1049
69.5793-3.9265-4.53336.39475.16674.43340.04350.3822-0.8510.2076-0.22170.02420.1466-0.24070.17830.3475-0.1193-0.19410.4011-0.16550.60479.11921.9999-5.6816
79.5258-2.5912.91996.7325-5.40444.42840.12750.4633-0.9658-0.5920.35360.62990.4744-0.2276-0.48110.1456-0.0891-0.02420.268-0.2160.838811.46990.95461.0193
82.45320.58580.43591.3361-0.97651.34470.07260.4071-0.1874-0.05740.06120.39070.0581-0.059-0.13380.03580.0406-0.02980.1804-0.19610.479316.40969.40731.7103
91.6826-0.3026-1.05822.2064-2.79775.8933-0.24550.05920.02910.250.02810.3121-0.076-0.44490.21740.16340.05070.16350.1785-0.12690.62086.082718.824418.871
105.27021.31292.94586.2824-1.70274.767-0.0178-0.8549-0.01720.9541-0.23460.2092-0.1753-0.26770.25240.40340.09780.33960.36350.02660.47313.91711.46629.645
116.9039-0.4528-4.04396.7891-0.63775.5259-0.2954-0.42080.16360.65760.17320.5147-0.08820.36140.12220.2410.04610.14520.1281-0.05620.275822.42615.156921.7257
121.79810.20630.63170.94580.08151.503-0.0516-0.0812-0.30480.2842-0.01270.42560.1026-0.16850.06430.16130.02810.16060.0897-0.03870.367218.57936.992315.6583
138.84355.6563-5.6729.2014-2.45324.19310.1350.0836-0.53490.153-0.36230.6786-0.11420.06110.22730.08480.01810.11850.2428-0.19820.686817.03773.24928.0509
147.8004-1.3945-4.76369.23182.68278.8263-0.26340.2789-0.66290.1792-0.21110.63520.6779-0.37070.47460.13280.00520.09040.1909-0.03450.387811.81975.183514.3449
151.1161-0.601-0.4550.42860.37790.9242-0.08620.15680.03240.0477-0.07510.1809-0.1125-0.04270.16130.15740.0410.02190.1162-0.0060.396123.394521.32958.1798
163.60711.6321-3.33110.9909-2.25215.67710.1726-0.12960.30440.2248-0.15220.1603-0.42750.3234-0.02040.2578-0.02590.09880.0975-0.08810.346727.442226.274313.5387
179.8395-3.0094-0.63031.8899-1.53073.1297-0.3367-0.2789-0.35510.33470.13350.0806-0.3431-0.06150.20330.18010.04390.16750.0933-0.10240.524315.095222.622118.1673
182.47260.04993.257.9096-3.29955.71490.0494-0.24670.05720.0346-0.01270.39390.0775-0.3681-0.03660.12750.03130.2530.273-0.10130.68284.081212.212716.8
191.5278-0.5083-0.5533.9776-3.52455.4167-0.1358-0.09240.4020.4781-0.0324-0.4916-0.46680.35790.16820.2012-0.0845-0.0960.101-0.01420.224650.723423.643512.4415
206.19790.35732.01721.33861.38642.1133-0.07270.29850.5849-0.1074-0.0670.1321-0.34710.00290.13970.3174-0.0420.00580.08070.11660.297243.032332.8636-2.1439
216.177-3.8402-0.10719.7301-5.08067.73940.01590.0940.60620.43970.0434-0.0225-0.85320.1272-0.05930.2498-0.0205-0.01980.01840.05640.270337.793232.97093.8505
221.8781-0.21480.19772.3422-1.4070.8515-0.1432-0.1110.31890.35810.14240.0131-0.2369-0.06860.00080.283-0.0218-0.00950.1201-0.02540.221139.786825.060310.432
232.5748-3.43860.62468.4175-0.15140.7762-0.3297-0.13750.12710.87540.32210.0492-0.04170.17980.00750.30350.0364-0.00240.1952-0.05440.125644.65116.144220.9607
243.7084-0.8759-1.00013.5862-4.87227.9949-0.1017-0.12350.20180.39-0.0175-0.1536-0.50820.10860.11920.2051-0.0114-0.0170.1285-0.02180.104951.39038.812518.7286
259.4119-1.6833.47556.13111.06212.6829-0.06340.28070.2193-0.123-0.1817-0.33080.0130.03640.2450.1861-0.01240.02170.17210.01660.105550.27587.389410.6207
260.5942-0.3676-0.06882.2401-0.1751.3652-0.1241-0.02810.13620.15640.07150.0896-0.10680.03680.05260.1592-0.01480.00270.13850.00770.119243.533413.27349.1602
271.7224-0.547-0.05662.30470.14662.2540.07980.18410.402-0.0865-0.0752-0.1505-0.25160.162-0.00460.2072-0.066-0.01880.14510.11240.17949.788425.6449-6.812
282.50641.37310.09841.68671.08992.26-0.18330.4067-0.0697-0.39870.1204-0.2285-0.12240.19290.06290.2227-0.00440.06940.22550.1130.154451.647111.2709-17.4971
294.5638-1.3196-1.78442.33611.03187.7130.20.30490.0919-0.4476-0.1594-0.0452-0.453-0.2254-0.04070.27270.0005-0.02920.19110.07080.120141.875514.3329-17.6532
305.5187-0.7981-5.58522.84330.41866.9453-0.29010.2436-0.1338-0.2685-0.11260.12150.2784-0.27410.40270.18560.0091-0.06650.23540.01670.186433.226413.0127-7.8019
313.2492-1.4632-1.09980.89850.73490.7886-0.12430.09890.0541-0.0347-0.00780.1425-0.0332-0.01960.13210.1748-0.01270.00120.15850.02390.153140.280112.5143-1.6942
327.0126-1.3144-1.32643.07541.23183.80950.00670.1815-0.2767-0.0489-0.0651-0.18880.13070.29280.05840.1666-0.0039-0.01510.18750.01790.100647.77564.308-7.7987
331.5344-0.35110.2972.1174-0.37370.9557-0.04740.08430.01660.0213-0.03480.0566-0.06120.04620.08230.1643-0.0217-0.00330.15980.0160.101543.636710.25560.0786
343.27121.05011.43323.27660.21790.6536-0.05060.00540.21590.0876-0.02910.2597-0.068-0.01290.07970.25670.050.00570.15670.02780.229931.477522.84881.9967
355.4668-0.4511-1.75851.36150.56221.799-0.00880.40660.1551-0.2388-0.09810.125-0.2881-0.18130.10680.21790.0209-0.05780.11930.09580.153736.693424.0638-8.0323
365.4618-1.23220.56655.1244-0.13424.177-0.08910.21780.1282-0.0333-0.1457-0.3681-0.31060.3690.23490.1395-0.0596-0.00320.17350.09660.158255.095116.4806-6.8514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 18
3X-RAY DIFFRACTION3A19 - 28
4X-RAY DIFFRACTION4A29 - 37
5X-RAY DIFFRACTION5A38 - 47
6X-RAY DIFFRACTION6A48 - 53
7X-RAY DIFFRACTION7A54 - 59
8X-RAY DIFFRACTION8A60 - 77
9X-RAY DIFFRACTION9A78 - 94
10X-RAY DIFFRACTION10A95 - 105
11X-RAY DIFFRACTION11A106 - 117
12X-RAY DIFFRACTION12A118 - 140
13X-RAY DIFFRACTION13A141 - 147
14X-RAY DIFFRACTION14A148 - 153
15X-RAY DIFFRACTION15A154 - 165
16X-RAY DIFFRACTION16A166 - 172
17X-RAY DIFFRACTION17A173 - 183
18X-RAY DIFFRACTION18A184 - 191
19X-RAY DIFFRACTION19B1 - 9
20X-RAY DIFFRACTION20B10 - 19
21X-RAY DIFFRACTION21B20 - 25
22X-RAY DIFFRACTION22B26 - 35
23X-RAY DIFFRACTION23B36 - 45
24X-RAY DIFFRACTION24B46 - 53
25X-RAY DIFFRACTION25B54 - 58
26X-RAY DIFFRACTION26B59 - 77
27X-RAY DIFFRACTION27B78 - 88
28X-RAY DIFFRACTION28B89 - 101
29X-RAY DIFFRACTION29B102 - 109
30X-RAY DIFFRACTION30B110 - 118
31X-RAY DIFFRACTION31B119 - 126
32X-RAY DIFFRACTION32B127 - 137
33X-RAY DIFFRACTION33B138 - 157
34X-RAY DIFFRACTION34B158 - 164
35X-RAY DIFFRACTION35B165 - 183
36X-RAY DIFFRACTION36B184 - 191

+
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://pdbjlvh1.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