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- PDB-6cys: Crystal structure analysis of the D150G mutant of Superoxide Dism... -

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Basic information

Entry
Database: PDB / ID: 6cys
TitleCrystal structure analysis of the D150G mutant of Superoxide Dismutase from Trichoderma reesei
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / enzymatic activity
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / 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 / Resolution: 1.85 Å
AuthorsMendoza Rengifo, E. / Garratt, R.C. / 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 analysis of the D150G mutant of Superoxide Dismutase from Trichoderma reesei
Authors: Mendoza Rengifo, E. / Garratt, R.C. / 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)92,5088
Polymers92,2844
Non-polymers2234
Water18,8081044
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-35 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 82.010, 133.610
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
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 212 / Label seq-ID: 3 - 211

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Superoxide dismutase /


Mass: 23071.055 Da / Num. of mol.: 4 / Mutation: D150G
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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1044 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM Bis-Tris pH 6.0, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→69.89 Å / Num. obs: 72428 / % possible obs: 97.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.063 / Rrim(I) all: 0.106 / Rsym value: 0.084 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.85-1.952.40.332106970.8540.0330.0550.04499.4
5.85-69.892.60.04421940.9970.0270.0470.03988.8

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→51.022 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.18
RfactorNum. reflection% reflection
Rfree0.1911 3627 5.01 %
Rwork0.1603 --
obs0.1618 72401 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.59 Å2 / Biso mean: 22.1019 Å2 / Biso min: 8.08 Å2
Refinement stepCycle: final / Resolution: 1.85→51.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 4 1044 7516
Biso mean--10.85 29.42 -
Num. residues----836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056648
X-RAY DIFFRACTIONf_angle_d0.7239044
X-RAY DIFFRACTIONf_chiral_restr0.047972
X-RAY DIFFRACTIONf_plane_restr0.0061156
X-RAY DIFFRACTIONf_dihedral_angle_d12.193864
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4991X-RAY DIFFRACTION6.822TORSIONAL
12B4991X-RAY DIFFRACTION6.822TORSIONAL
13C4991X-RAY DIFFRACTION6.822TORSIONAL
14D4991X-RAY DIFFRACTION6.822TORSIONAL
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 (%)
1.85-1.87440.25521250.22482692281799
1.8744-1.90.22441460.21132673281999
1.9-1.92720.23041360.20632666280299
1.9272-1.95590.23231330.19212689282299
1.9559-1.98650.23111280.17762683281199
1.9865-2.01910.22441630.18722668283199
2.0191-2.05390.24411420.18192648279099
2.0539-2.09120.2281540.16992692284699
2.0912-2.13150.21471630.16582629279299
2.1315-2.1750.19851410.17272665280699
2.175-2.22230.18241340.15822693282798
2.2223-2.2740.18191520.15442651280398
2.274-2.33080.20321410.15592658279998
2.3308-2.39390.18931150.15832669278498
2.3939-2.46430.21331420.15462659280198
2.4643-2.54380.18751280.15042668279697
2.5438-2.63470.19081300.15232643277397
2.6347-2.74020.19211680.15492625279397
2.7402-2.86490.16611420.15512621276396
2.8649-3.0160.18631250.15492648277396
3.016-3.20490.18911440.15262602274695
3.2049-3.45230.18941210.15412655277695
3.4523-3.79960.16931540.15082578273294
3.7996-4.34920.14911470.13232604275193
4.3492-5.47850.17351170.13972575269291
5.4785-51.04130.18771360.18312520265686
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)
11.8613-0.2688-0.44281.43320.40791.7756-0.0478-0.31830.24550.21190.16960.1492-0.24180.1396-0.05920.19370.03210.04280.19730.01270.1416-0.2022-10.7258-17.7812
21.41-0.02470.06061.59680.27111.4284-0.137-0.02480.18870.22120.0779-0.261-0.18170.40460.01570.1906-0.0006-0.01380.21080.03480.19539.1294-9.761-20.405
31.415-0.0458-0.3460.62730.24791.6232-0.03750.172-0.0725-0.03640.01340.13780.0853-0.04270.01460.1075-0.00530.00680.10740.02490.13470.8379-22.2457-39.4772
40.1955-0.1109-0.57620.1459-0.05171.897-0.0291-0.1053-0.1089-0.0418-0.0605-0.04680.0290.3306-0.03760.1404-0.00290.00860.17870.04640.167911.5001-19.3531-37.2597
50.5085-0.31010.25910.7196-0.55031.8737-0.01360.0142-0.0005-0.02230.02440.05130.01750.0104-0.01240.09840.00430.01540.11590.02660.15930.0352-21.8063-30.4766
60.81580.28130.57720.67810.69062.8722-0.06640.07270.2953-0.0506-0.00420.0079-0.4206-0.1823-0.0220.1798-0.0154-0.01480.18010.04340.28724.9129-3.5357-32.2952
71.72820.03240.01321-0.23090.3220.03990.05180.3144-0.0369-0.0071-0.0749-0.0995-0.025-0.01560.1388-0.01640.03320.0914-0.00290.13838.6417-5.0201-30.5253
82.3115-1.58950.54542.0898-0.11310.36990.0591-0.07260.0393-0.043-0.01710.2095-0.0922-0.0782-0.04920.14120.00860.03610.099-0.00440.142229.3303-6.5789-28.1573
90.71150.0402-0.13971.0538-0.70010.84620.0058-0.1087-0.08430.0262-0.0397-0.08470.09820.05120.00790.1332-0.0040.01740.09880.00130.128238.8438-27.7267-21.3578
100.35830.3996-0.05841.1287-0.94261.0834-0.01180.0114-0.07010.04480.02390.0487-0.0317-0.1264-0.03430.1039-0.00820.02360.1015-0.01090.11934.327-20.7674-29.2567
111.28820.1034-0.85831.1308-0.7031.6136-0.005-0.0663-0.2159-0.022-0.0997-0.16990.13350.11020.0640.0999-0.00660.01410.07920.00470.18143.187-24.1866-22.7001
120.6869-0.0590.11843.3786-0.91981.01060.0042-0.7155-0.080.95930.00880.0763-0.5653-0.7292-0.08440.40540.03610.01450.424-0.07260.229932.453-8.3108-15.5342
130.5110.03050.11190.7314-0.12711.5423-0.14060.269-0.2427-0.2570.1259-0.27930.07120.1095-0.00980.1608-0.03430.05410.1719-0.06210.139135.6737-24.0156-56.9575
141.26460.5697-0.48322.4801-0.54661.1498-0.01520.1901-0.27120.08010.1192-0.1387-0.0468-0.0749-0.09190.108-0.0029-0.00280.1098-0.0350.093122.0788-37.2367-43.9791
150.71730.13180.08611.3558-0.62660.2144-0.09650.2693-0.0107-0.11780.16590.002-0.0173-0.1397-0.05550.156-0.0240.01630.1661-0.02890.104423.9482-22.7681-52.9884
160.63690.2088-0.47422.15771.35493.42790.05180.4760.384-0.24740.08060.5292-0.3511-0.5123-0.0850.27550.023-0.0410.34960.14050.264616.5043-2.578-62.5866
171.2107-0.31241.06231.5767-1.75183.8206-0.1520.18460.4348-0.17560.0568-0.1004-0.4308-0.02850.04110.2597-0.0160.02440.15320.0440.269225.0225-2.3852-52.482
181.020.18430.31150.9173-0.0021.89710.00820.24060.0077-0.06160.11130.127-0.0784-0.1185-0.07580.15410.0046-0.00610.15780.02330.145321.1278-12.9606-49.0295
191.7838-1.03971.52681.5847-0.80651.8178-0.1034-0.08270.06690.21010.26810.2933-0.4434-0.5439-0.12820.16710.01650.03560.21550.05640.216715.9827-10.4342-50.8465
200.41390.4537-0.10280.83310.04330.9294-0.01160.08370.0572-0.02290.05880.0193-0.0804-0.0701-0.0460.1392-0.01440.02790.12120.00850.109228.781-15.4229-48.8189
211.4053-0.13740.75310.491-0.16841.2083-0.07620.29980.2671-0.2070.06170.0183-0.1683-0.0132-0.02890.2131-0.03960.03110.21450.02570.135127.79-10.6763-59.6686
220.3619-0.7260.53393.2528-2.23661.53260.09870.5053-0.0838-0.46420.15640.47320.224-0.1675-0.19750.2511-0.0584-0.02280.35160.00110.213514.3168-25.18-57.3409
231.15660.1320.4950.9907-0.65341.97070.0999-0.1169-0.25020.03540.06170.06020.1778-0.1654-0.11150.1205-0.01540.01180.13120.04660.1524.4514-41.9949-9.8432
240.2978-0.0574-1.43660.05360.40571.83480.0329-0.044-0.02390.0041-0.004-0.0072-0.04120.0797-0.02890.13020.02880.00250.14240.01070.129618.5558-40.0399-24.3351
250.72720.08230.23490.573-0.30890.78360.0817-0.5903-0.23570.2187-0.046-0.1503-0.1393-0.20250.02650.2058-0.02390.02910.28260.07510.130316.599-33.73897.2441
261.4332-0.52081.19880.6187-0.68643.9112-0.2541-0.40670.27470.30380.1179-0.0145-0.3188-0.360.09910.26740.04270.05090.1763-0.04250.17714.1715-22.08150.9493
271.4085-0.14630.30880.8558-0.21091.27830.018-0.12410.07040.0978-0.0325-0.0176-0.11440.02080.01930.1212-0.00190.0320.12270.02260.109313.9435-30.0964-5.8751
280.22590.5350.92050.97661.7523.18680.3007-0.0905-0.65970.10540.2866-0.20160.41020.6015-0.46220.25940.0294-0.02830.40230.0360.412825.8935-42.156-10.0367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 57 )A4 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 83 )A58 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 137 )A84 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 147 )A138 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 197 )A148 - 197
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 212 )A198 - 212
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 57 )B4 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 83 )B58 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 137 )B84 - 137
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 176 )B138 - 176
11X-RAY DIFFRACTION11chain 'B' and (resid 177 through 198 )B177 - 198
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 212 )B199 - 212
13X-RAY DIFFRACTION13chain 'C' and (resid 4 through 33 )C4 - 33
14X-RAY DIFFRACTION14chain 'C' and (resid 34 through 57 )C34 - 57
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 98 )C58 - 98
16X-RAY DIFFRACTION16chain 'C' and (resid 99 through 111 )C99 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 125 )C112 - 125
18X-RAY DIFFRACTION18chain 'C' and (resid 126 through 137 )C126 - 137
19X-RAY DIFFRACTION19chain 'C' and (resid 138 through 147 )C138 - 147
20X-RAY DIFFRACTION20chain 'C' and (resid 148 through 176 )C148 - 176
21X-RAY DIFFRACTION21chain 'C' and (resid 177 through 197 )C177 - 197
22X-RAY DIFFRACTION22chain 'C' and (resid 198 through 212 )C198 - 212
23X-RAY DIFFRACTION23chain 'D' and (resid 4 through 33 )D4 - 33
24X-RAY DIFFRACTION24chain 'D' and (resid 34 through 83 )D34 - 83
25X-RAY DIFFRACTION25chain 'D' and (resid 84 through 111 )D84 - 111
26X-RAY DIFFRACTION26chain 'D' and (resid 112 through 125 )D112 - 125
27X-RAY DIFFRACTION27chain 'D' and (resid 126 through 197 )D126 - 197
28X-RAY DIFFRACTION28chain 'D' and (resid 198 through 212 )D198 - 212

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