[English] 日本語
Yorodumi
- PDB-5tir: Crystal Structure of Mn Superoxide Dismutase mutant M27V from Tri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tir
TitleCrystal Structure of Mn Superoxide Dismutase mutant M27V from Trichoderma reesei
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / mitochondrion / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsMendoza, E.R. / Brandao-Neto, J. / Pereira, H.M. / Ferreira Junior, J.R.S. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/01855-2 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Mn Superoxide Dismutase mutant M27V from Trichoderma reesei
Authors: Mendoza, E.R. / Brandao-Neto, J. / Pereira, H.M. / Ferreira Junior, J.R.S. / Penner-Hahn, J.E. / Garratt, R.C.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,1338
Polymers92,9134
Non-polymers2204
Water17,583976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-54 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 77.640, 159.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0
411chain D and segidD0

-
Components

#1: Protein
Superoxide dismutase


Mass: 23228.223 Da / Num. of mol.: 4 / Mutation: M27V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: TRIREDRAFT_66345 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: G0RQS7, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 100mM Bis-Tris pH 6.3, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.62→55.55 Å / Num. obs: 107813 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.62-1.666.51.2410.525199.9
7.24-55.555.80.019199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KKC

1kkc


Resolution: 1.62→48.734 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.36
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2000 1.86 %Random Selection
Rwork0.1623 ---
obs0.1628 107720 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.16 Å2 / Biso mean: 26.2456 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.62→48.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 4 976 7409
Biso mean--17.57 36.47 -
Num. residues----829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076609
X-RAY DIFFRACTIONf_angle_d1.0789003
X-RAY DIFFRACTIONf_chiral_restr0.045973
X-RAY DIFFRACTIONf_plane_restr0.0061153
X-RAY DIFFRACTIONf_dihedral_angle_d11.8952313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3861X-RAY DIFFRACTION2.955TORSIONAL
12B3861X-RAY DIFFRACTION2.955TORSIONAL
13C3861X-RAY DIFFRACTION2.955TORSIONAL
14D3861X-RAY DIFFRACTION2.955TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.62-1.66050.29421400.268574457585
1.6605-1.70540.27581420.253274607602
1.7054-1.75560.27151410.234874527593
1.7556-1.81230.24461410.214574737614
1.8123-1.8770.22121420.203274947636
1.877-1.95220.20171410.181474857626
1.9522-2.0410.21651430.166775107653
2.041-2.14870.19941420.160475227664
2.1487-2.28330.18571420.149875397681
2.2833-2.45960.16031430.151175457688
2.4596-2.70710.18921430.153375617704
2.7071-3.09870.1841450.161776207765
3.0987-3.90380.16751450.149576527797
3.9038-48.75580.14751500.135779628112
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)
11.067-0.32850.40351.4589-0.73531.12590.0327-0.0409-0.13810.00060.06190.12660.0479-0.1397-0.09820.1257-0.02170.00130.1703-0.00980.1452.7662-20.584-7.091
22.007-1.1022-0.45532.84190.12941.13410.16210.3958-0.2001-0.3737-0.2084-0.10680.11320.10140.07780.16530.03120.01440.238-0.02860.154922.4341-24.3278-15.0066
31.4736-0.6232-0.43891.9447-0.03470.8950.09660.2266-0.1834-0.2595-0.08750.10710.1015-0.098-0.03860.13680.0027-0.02420.1688-0.01560.150713.9326-24.3099-8.8719
42.96550.4833-2.43070.9777-0.32244.55030.0661-0.20070.02550.1683-0.1062-0.1284-0.24680.31280.03720.1859-0.0163-0.05280.13150.01410.162826.9231-0.17533.9557
52.203-0.7029-2.15641.4650.97814.16170.0166-0.08870.07240.1724-0.04470.0082-0.23780.05720.02480.1614-0.0183-0.03570.09940.00710.131421.74255.121-1.1404
68.77061.78321.08741.10451.21425.82470.0674-0.01670.97870.1690.20580.3931-1.0483-0.3308-0.11660.46820.15790.12020.26870.06340.37211.970919.0641.5607
76.1529-3.644-1.60569.23824.06755.88230.0440.1621-0.04490.0904-0.19110.9765-0.1905-0.961-0.03760.18350.06880.04990.28180.04490.22760.3055.97821.0345
83.24-1.66160.17184.652-0.65413.46460.15120.26810.4102-0.3317-0.0381-0.0358-0.389-0.135-0.150.20280.03640.03340.1810.0390.16919.85257.1982-5.6653
93.0691-1.1073-1.67272.10332.15873.02760.20220.37520.3257-0.437-0.0853-0.0829-0.6022-0.1519-0.0750.28450.02620.01630.21220.0360.180315.39867.2064-4.2902
102.86261.0107-1.17513.4819-2.16153.3528-0.01430.0124-0.1170.10260.02370.10560.0084-0.1085-0.11110.15920.0067-0.00290.1548-0.00670.147610.5693-8.1465.597
113.05461.87340.82246.6890.05581.51880.117-0.07510.11350.3025-0.10030.315-0.3435-0.4549-0.06790.24730.0270.05880.22830.02110.19065.19390.86168.614
123.8812-1.6159-1.18263.5357-0.60963.93410.162-0.1450.64710.4545-0.0078-0.1069-0.59130.1802-0.22160.39760.01860.05290.1461-0.01280.243913.032816.73946.2839
139.2799-0.82715.11094.44491.02763.3587-0.35280.56260.40060.71730.1972-0.2069-1.01910.48150.51260.6723-0.09170.04740.40230.0070.409323.070316.725-1.9528
140.2436-0.10220.58013.1319-1.67721.8956-0.08860.10390.1655-0.24330.29090.38310.1138-0.3577-0.16910.20120.0431-0.01630.22820.00140.21-4.35288.748-40.7402
150.81740.7789-0.34964.6619-3.20462.4877-0.02040.02550.0079-0.38480.10550.15210.3387-0.1153-0.05460.2116-0.0032-0.02210.1786-0.01870.1406-2.0263-3.7143-36.2837
160.7480.00160.19253.3088-1.58951.2072-0.0128-0.08530.14230.1048-0.05570.0852-0.0486-0.17280.0450.13480.0121-0.0080.1871-0.05530.1422-1.83334.5033-29.7315
171.8999-0.5876-0.20381.465-1.08631.0803-0.0873-0.50750.41550.7936-0.23090.4439-0.674-0.3065-0.01210.38750.11440.01760.3386-0.28170.39220.475326.3085-18.8238
182.4095-1.9216-1.74866.71982.27142.3524-0.0176-0.29360.57150.4294-0.0789-0.569-0.28660.1092-0.00450.257-0.0075-0.06220.1976-0.04910.27810.858121.2404-25.0081
195.124-1.9645-0.89113.91990.4582.5942-0.1314-0.39650.13210.42610.03880.2385-0.0498-0.10970.17270.18430.00830.02030.1959-0.03380.1666.053810.3923-24.0578
202.08610.93880.44623.04611.41025.2947-0.1827-0.73960.19020.95760.16730.6858-0.03780.13830.01050.31110.00390.06660.2834-0.06260.21784.593612.6875-18.6949
212.3436-1.75060.27124.45830.66010.9777-0.1287-0.48330.02610.80540.02260.30670.0702-0.26510.07360.23530.0040.04070.2523-0.03330.16651.48148.196-24.3676
221.2198-0.0137-0.0922.8201-0.58742.3292-0.00780.08110.0885-0.0977-0.1012-0.1606-0.0788-0.02340.1090.15760.03560.01590.16380.01040.183612.906710.1579-39.2176
236.8892-1.31810.4494.25690.8523.0242-0.098-0.15080.58440.0093-0.1465-0.0417-0.33170.020.29930.21440.0085-0.01680.16540.0060.19739.277619.6419-35.3388
240.4487-0.6815-0.9612.74940.29463.1331-0.1392-0.1940.45140.0397-0.10320.456-0.0908-0.8580.12510.22050.09040.00690.3732-0.16470.3699-6.413220.1214-27.0085
259.4993-2.5026-1.52252.0061-2.64249.30750.9763-0.93850.03320.58410.10170.7646-0.8298-0.8423-0.92560.56980.00680.16010.7761-0.09960.7143-10.84018.2271-23.1786
260.48960.1614-0.07411.0306-0.27422.58530.02060.0156-0.01280.01030.0011-0.1517-0.35760.2342-0.05450.1455-0.020.00180.16750.02180.198830.15263.3221-33.6641
272.7441-2.2722-0.77015.88361.08662.2447-0.038-0.0782-0.3410.24180.1048-0.03260.37350.0121-0.04140.19110.0023-0.00780.1330.03320.199922.4368-16.5841-34.8125
282.0129-0.89510.45182.12450.2351.54610.050.0101-0.08170.0319-0.0057-0.13280.09230.0185-0.04340.1389-0.00320.02370.13760.01910.165523.5599-7.1357-39.1164
295.3916-1.2176-5.65398.60953.57989.51170.148-0.4921-0.33030.31730.1563-0.94580.15761.5668-0.33210.42750.0834-0.07060.58930.02490.512738.5417-8.1761-28.799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 98 )A2 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 147 )A99 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 209 )A148 - 209
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 54 )B2 - 54
5X-RAY DIFFRACTION5chain 'B' and (resid 55 through 98 )B55 - 98
6X-RAY DIFFRACTION6chain 'B' and (resid 99 through 111 )B99 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 125 )B112 - 125
8X-RAY DIFFRACTION8chain 'B' and (resid 126 through 147 )B126 - 147
9X-RAY DIFFRACTION9chain 'B' and (resid 148 through 163 )B148 - 163
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 176 )B164 - 176
11X-RAY DIFFRACTION11chain 'B' and (resid 177 through 187 )B177 - 187
12X-RAY DIFFRACTION12chain 'B' and (resid 188 through 198 )B188 - 198
13X-RAY DIFFRACTION13chain 'B' and (resid 199 through 208 )B199 - 208
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 23 )C2 - 23
15X-RAY DIFFRACTION15chain 'C' and (resid 24 through 54 )C24 - 54
16X-RAY DIFFRACTION16chain 'C' and (resid 55 through 98 )C55 - 98
17X-RAY DIFFRACTION17chain 'C' and (resid 99 through 111 )C99 - 111
18X-RAY DIFFRACTION18chain 'C' and (resid 112 through 125 )C112 - 125
19X-RAY DIFFRACTION19chain 'C' and (resid 126 through 137 )C126 - 137
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 147 )C138 - 147
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 163 )C148 - 163
22X-RAY DIFFRACTION22chain 'C' and (resid 164 through 176 )C164 - 176
23X-RAY DIFFRACTION23chain 'C' and (resid 177 through 187 )C177 - 187
24X-RAY DIFFRACTION24chain 'C' and (resid 188 through 198 )C188 - 198
25X-RAY DIFFRACTION25chain 'C' and (resid 199 through 208 )C199 - 208
26X-RAY DIFFRACTION26chain 'D' and (resid 2 through 98 )D2 - 98
27X-RAY DIFFRACTION27chain 'D' and (resid 99 through 147 )D99 - 147
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 198 )D148 - 198
29X-RAY DIFFRACTION29chain 'D' and (resid 199 through 208 )D199 - 208

+
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