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- PDB-3t5w: 2ME modified human SOD1 -

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Basic information

Entry
Database: PDB / ID: 3t5w
Title2ME modified human SOD1
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / 2ME modification at Cys111
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / cellular response to cadmium ion / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / positive regulation of cytokine production / placenta development / determination of adult lifespan / regulation of mitochondrial membrane potential / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIhara, K. / Yamaguchi, Y. / Torigoe, H. / Wakatsuki, S. / Taniguchi, N. / Suzuki, K. / Fujiwara, N.
CitationJournal: Biosci.Rep. / Year: 2012
Title: Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme
Authors: Ihara, K. / Fujiwara, N. / Yamaguchi, Y. / Torigoe, H. / Wakatsuki, S. / Taniguchi, N. / Suzuki, K.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,54448
Polymers190,84412
Non-polymers2,70036
Water31,4541746
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-43 kcal/mol
Surface area13940 Å2
MethodPISA
2
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-43 kcal/mol
Surface area14040 Å2
MethodPISA
3
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-43 kcal/mol
Surface area13990 Å2
MethodPISA
4
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-42 kcal/mol
Surface area14030 Å2
MethodPISA
5
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-44 kcal/mol
Surface area13980 Å2
MethodPISA
6
L: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2578
Polymers31,8072
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-43 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.086, 163.277, 173.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Superoxide dismutase [Cu-Zn] / copper zinc superoxide dismutase / Superoxide dismutase 1 / hSod1


Mass: 15903.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1746 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 3350, 300mM (NH4)2SO4, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→118.7 Å / Num. all: 195308 / Num. obs: 185279 / % possible obs: 94.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.115 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 17868 / Rsym value: 0.882 / % possible all: 88.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1p1v

1p1v


Resolution: 1.8→34.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.564 / SU ML: 0.092 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 9252 5 %RANDOM
Rwork0.19976 ---
obs0.20181 175704 94.87 %-
all-184956 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--1.22 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13368 0 84 1746 15198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02113644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.95418408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72725.625576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6971548
X-RAY DIFFRACTIONr_chiral_restr0.0870.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110344
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6731.58940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23214208
X-RAY DIFFRACTIONr_scbond_it1.99234704
X-RAY DIFFRACTIONr_scangle_it3.3654.54200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 683 -
Rwork0.276 12534 -
obs--92.5 %
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)
10.2828-0.08450.00510.3490.08880.49560.00130.0358-0.05860.0028-0.0145-0.0102-0.02990.02180.01320.3014-0.0080.0060.3164-0.0380.370116.181220.674-32.8619
20.482-0.0201-0.13490.36220.04140.4409-0.005-0.01230.00690.0110.0003-0.0306-0.0119-0.03610.00470.32320.0008-0.00740.3134-0.01860.341413.854242.1128-14.8219
30.11560.0248-0.07260.7610.17060.2549-0.01080.0064-0.00660.0012-0.01250.05590.0133-0.00250.02330.307-0.0017-0.00220.3237-0.02060.355652.723822.6185-30.3196
40.4893-0.1048-0.24990.451-0.02690.37960.0226-0.01480.02830.0115-0.0091-0.0056-0.03110.0187-0.01360.3165-0.01480.00360.3159-0.0160.34850.283449.1757-20.9185
50.4980.0110.02370.71420.09120.34160.04940.03350.02220.1154-0.05880.07270.04130.00060.00940.3533-0.02380.02190.2847-0.03890.338216.3978-10.5228-38.5758
60.1582-0.26580.16770.8610.03840.49020.0596-0.0255-0.0040.0832-0.03980.08050.0993-0.0222-0.01970.4469-0.08290.02120.2555-0.01960.301915.0907-36.8038-28.7806
70.67940.4046-0.08250.6553-0.08280.74290.0536-0.0628-0.09940.0501-0.0749-0.0870.0861-0.00160.02120.3672-0.0203-0.02670.2820.02110.329350.1706-7.9051-24.7035
80.78820.4729-0.28151.44150.31111.00610.034-0.1365-0.16050.2284-0.1164-0.07390.16360.07870.08240.4648-0.0389-0.0410.26610.11150.288243.281-28.2269-6.2239
90.51260.0941-0.09950.8147-0.17540.94670.02480.0793-0.0177-0.0445-0.07520.0888-0.02050.04090.05040.2990.0396-0.02090.3607-0.03640.310122.51319.2886-61.9096
100.8459-0.0635-0.00170.80260.35761.47880.00460.2871-0.0639-0.1263-0.03420.1184-0.23760.19970.02960.37970.0403-0.04120.50320.01090.152529.55913.0932-88.5014
111.3603-0.22580.06080.45990.11050.40.04460.3251-0.04740.0711-0.0820.0074-0.00110.01860.03740.30290.024-0.0050.3898-0.03790.298257.43771.9947-53.9087
121.823-0.67030.10291.3527-0.93741.10210.19261.1576-0.1065-0.0708-0.2079-0.01010.07390.24490.01530.18030.1917-0.00651.2178-0.20010.079462.1522-2.7915-81.0306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION2B1 - 153
3X-RAY DIFFRACTION3D1 - 153
4X-RAY DIFFRACTION4E1 - 153
5X-RAY DIFFRACTION5F1 - 153
6X-RAY DIFFRACTION6G1 - 153
7X-RAY DIFFRACTION7H1 - 153
8X-RAY DIFFRACTION8I1 - 153
9X-RAY DIFFRACTION9J1 - 153
10X-RAY DIFFRACTION10K1 - 153
11X-RAY DIFFRACTION11L1 - 153
12X-RAY DIFFRACTION12M1 - 153

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