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- PDB-6cyl: Crystal Structure of Superoxide Dismutase double mutant (G74Q+Q14... -

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Basic information

Entry
Database: PDB / ID: 6cyl
TitleCrystal Structure of Superoxide Dismutase double mutant (G74Q+Q149G) from Trichoderma reesei
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / enzymatic activity
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 / Resolution: 1.8 Å
AuthorsMendoza Rengifo, E. / Garratt, R.C. / Pereira, H.M. / Ferreira Jr., J.R.S.
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 double mutant (G74Q+Q149G) from Trichoderma reesei
Authors: Mendoza Rengifo, E. / Garratt, R.C. / Pereira, H.M. / Ferreira Jr., J.R.S.
History
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: 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 / 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,7368
Polymers92,5164
Non-polymers2204
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-45 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.571, 78.433, 158.283
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
11(chain A and resid 5 through 198)
21(chain B and resid 5 through 198)
31(chain C and resid 5 through 198)
41(chain D and resid 5 through 198)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 5 - 198 / Label seq-ID: 4 - 197

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 5 through 198)AA
2(chain B and resid 5 through 198)BB
3(chain C and resid 5 through 198)CC
4(chain D and resid 5 through 198)DD

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Components

#1: Protein
Superoxide dismutase


Mass: 23129.090 Da / Num. of mol.: 4 / Mutation: G74Q, Q149G
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 BL21(DE3) (bacteria) / References: UniProt: G0RQS7, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% polyethylene glycol (PEG) 3350, 0.1 mM Bis-Tris, pH 6.5
PH range: 5.5-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→79.14 Å / Num. obs: 72980 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.21 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.8-1.8440.64942630.671199.7
9-79.143.70.0556620.991197.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
PHENIXmodel building
PHASERphasing
PDB_EXTRACTV3.24data extraction
SCALAdata scaling
RefinementResolution: 1.8→79.14 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.66
RfactorNum. reflection% reflection
Rfree0.2612 3624 4.97 %
Rwork0.2422 --
obs0.2432 72899 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.33 Å2 / Biso mean: 18.3684 Å2 / Biso min: 3.93 Å2
Refinement stepCycle: final / Resolution: 1.8→79.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6093 0 4 678 6775
Biso mean--9.14 21.7 -
Num. residues----787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026269
X-RAY DIFFRACTIONf_angle_d0.4928546
X-RAY DIFFRACTIONf_chiral_restr0.039921
X-RAY DIFFRACTIONf_plane_restr0.0041092
X-RAY DIFFRACTIONf_dihedral_angle_d9.2783630
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3660X-RAY DIFFRACTION5.676TORSIONAL
12B3660X-RAY DIFFRACTION5.676TORSIONAL
13C3660X-RAY DIFFRACTION5.676TORSIONAL
14D3660X-RAY DIFFRACTION5.676TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82370.3591520.348726182770100
1.8237-1.84870.35371250.33232598272399
1.8487-1.87510.34371480.312926342782100
1.8751-1.90310.28981300.27682637276799
1.9031-1.93280.27631370.267626122749100
1.9328-1.96450.31551360.28626522788100
1.9645-1.99840.31311220.272426422764100
1.9984-2.03470.28941390.270926132752100
2.0347-2.07390.29381330.27526622795100
2.0739-2.11620.321260.276926442770100
2.1162-2.16220.28181170.268626842801100
2.1622-2.21250.311490.261426092758100
2.2125-2.26790.31851460.269926552801100
2.2679-2.32920.3151410.27226642805100
2.3292-2.39770.28881730.265426142787100
2.3977-2.47510.31341360.261526412777100
2.4751-2.56360.2951500.262226432793100
2.5636-2.66630.26041530.25926502803100
2.6663-2.78760.28531360.262426972833100
2.7876-2.93460.28591310.250726872818100
2.9346-3.11840.2771380.246326722810100
3.1184-3.35920.22541330.227927032836100
3.3592-3.69730.22551410.219627162857100
3.6973-4.23220.19121600.181226992859100
4.2322-5.3320.17331530.166227432896100
5.332-79.21810.15971190.17052886300599
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)
11.1351-0.0987-0.43020.6114-0.21060.90610.16010.14850.1994-0.096-0.00580.0412-0.0049-0.0262-0.05940.05340.03170.00040.10760.04540.1238131.2646339.9348158.7089
20.91380.2039-0.39530.7614-0.60850.77620.09420.00530.05380.0150.02210.0916-0.006-0.0196-0.07890.02440.0182-0.02770.0735-0.00620.0585123.0194326.9587171.7701
30.71790.10070.39440.52420.2020.41270.0167-0.22710.32060.1818-0.0939-0.0673-0.2160.1720.10840.1246-0.0687-0.00520.2364-0.08060.2228145.9111348.5705174.0305
41.10480.95160.47832.57090.78330.67410.0626-0.07950.07210.1016-0.0904-0.2828-0.04840.2244-0.00080.0763-0.0295-0.0220.30770.00430.1624151.5419336.4667171.5729
51.44820.27940.52832.79710.45790.89940.0783-0.26970.11330.3754-0.0813-0.15530.06810.0461-0.04260.063-0.0123-0.03790.1672-0.04230.0758141.7961332.5093176.6953
61.14560.22010.23061.39030.06290.0465-0.0342-0.09440.05830.134-0.02340.00710.0271-0.0024-0.05230.02470.0132-0.01030.1273-0.02310.0574139.5051331.7129166.4636
71.6567-0.32040.0551.22680.60130.60210.04080.02510.1359-0.0070.0475-0.174-0.00590.0875-0.00140.033-0.0030.0180.1371-0.03450.1231147.1499338.6374162.489
80.32880.3010.70032.3378-0.42642.04390.0955-0.26690.32670.3747-0.03560.1775-0.219-0.1498-0.06780.126-0.01130.02250.1799-0.09630.1851138.0354347.8831176.3486
90.90680.29040.11190.5670.16951.2686-0.07360.0171-0.1707-0.08450.054-0.193-0.0660.0545-0.00310.0662-0.00630.03630.0754-0.02780.139149.4429312.1839157.302
100.90060.76690.70311.90041.26231.50570.0387-0.1765-0.21220.2193-0.11290.2150.3414-0.33540.03170.1169-0.05970.04690.1432-0.02190.199129.8325304.254159.8936
111.50480.85751.07872.4831.84682.82270.0382-0.1901-0.35650.42760.0883-0.13850.474-0.0693-0.14020.11440.03510.0010.1037-0.00350.164139.6394306.4408162.8982
120.45760.57310.31792.18160.15750.7913-0.06020.0136-0.1863-0.08280.02160.16930.0907-0.17740.03480.0584-0.04650.01630.1251-0.02740.1126134.7439312.3338152.0203
130.42480.15340.13981.0259-0.3940.58140.0436-0.1112-0.03820.02610.09670.15240.1391-0.2189-0.10270.147-0.0209-0.00970.13150.02250.0695120.6509308.0386195.1513
140.50270.26180.02971.0880.02510.37630.0461-0.05-0.1008-0.17660.02180.07710.2351-0.1102-0.09030.1859-0.0217-0.0260.11880.02780.0522122.3825306.0597186.4639
150.47110.24780.10340.1994-0.00540.07440.0150.1379-0.1711-0.10420.0928-0.09090.23120.040.00170.4587-0.0217-0.03660.1819-0.08660.1919126.3795286.0336172.844
162.43123.71772.0436.69643.77072.1301-0.02090.1346-0.5121-0.17160.0441-0.41490.388-0.0669-0.0410.43940.0142-0.02430.1242-0.02270.2232136.0897290.5152180.5851
171.9180.63920.32811.77271.32351.0019-0.05990.2680.0334-0.33440.13320.12250.0340.2007-0.0380.2258-0.0418-0.05940.1172-0.00820.0815128.7057301.4779179.1426
180.15980.09780.01640.20210.26090.44930.0478-0.0118-0.1273-0.04190.0610.01210.4341-0.1075-0.17830.2819-0.0589-0.09060.10910.03090.1068129.9124293.991189.6742
190.11690.1286-0.10960.2141-0.30580.5541-0.0089-0.1455-0.09170.0519-0.1271-0.21840.1690.355-0.16690.16320.0614-0.08540.21350.11220.2298153.288305.3713190.6716
200.24080.28380.30490.33150.35710.381-0.1466-0.04550.20410.3138-0.0503-0.3122-0.42710.18920.05190.5359-0.0785-0.25160.2171-0.00660.3727148.1678327.1321203.8183
211.34340.39261.06690.72030.33151.631-0.17760.18360.3271-0.0092-0.0914-0.1648-0.41070.39420.26080.1992-0.0805-0.14180.2640.09730.2208147.4763321.2249191.0728
220.64620.26620.49390.41810.03980.545-0.0769-0.13040.33010.1716-0.171-0.18-0.47810.24820.2050.294-0.0947-0.15060.20090.02130.2305145.4847316.0768202.5997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 33 )A5 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 84 )A34 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 111 )A85 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 125 )A112 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 147 )A126 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 176 )A148 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 187 )A177 - 187
8X-RAY DIFFRACTION8chain 'A' and (resid 188 through 200 )A188 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 98 )B2 - 98
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 147 )B99 - 147
11X-RAY DIFFRACTION11chain 'B' and (resid 148 through 163 )B148 - 163
12X-RAY DIFFRACTION12chain 'B' and (resid 164 through 198 )B164 - 198
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 54 )C2 - 54
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 98 )C55 - 98
15X-RAY DIFFRACTION15chain 'C' and (resid 99 through 111 )C99 - 111
16X-RAY DIFFRACTION16chain 'C' and (resid 112 through 125 )C112 - 125
17X-RAY DIFFRACTION17chain 'C' and (resid 126 through 163 )C126 - 163
18X-RAY DIFFRACTION18chain 'C' and (resid 164 through 198 )C164 - 198
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 84 )D3 - 84
20X-RAY DIFFRACTION20chain 'D' and (resid 85 through 125 )D85 - 125
21X-RAY DIFFRACTION21chain 'D' and (resid 126 through 163 )D126 - 163
22X-RAY DIFFRACTION22chain 'D' and (resid 164 through 199 )D164 - 199

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