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- PDB-3kh3: Crystal structure of human Cu/Zn superoxide dismutase recombinant... -

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Basic information

Entry
Database: PDB / ID: 3kh3
TitleCrystal structure of human Cu/Zn superoxide dismutase recombinantly produced in Leishmania tarantolae; P212121 crystal form containing 12 chains in the asymmetric unit
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / eukaryotic expression / Leishmania tarantolae / Amyotrophic lateral sclerosis / Antioxidant / Disease mutation / Disulfide bond / Metal-binding / Neurodegeneration / Phosphoprotein
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 / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / 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 / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / 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 (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsGazdag, E.M. / Blankenfeldt, W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Purification and crystallization of human Cu/Zn superoxide dismutase recombinantly produced in the protozoan Leishmania tarentolae.
Authors: Gazdag, E.M. / Cirstea, I.C. / Breitling, R. / Lukes, J. / Blankenfeldt, W. / Alexandrov, K.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_alt_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_ptnr2_label_alt_id / _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_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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]
C: 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,76639
Polymers189,93112
Non-polymers1,83627
Water00
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1058
Polymers31,6552
Non-polymers4506
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-30 kcal/mol
Surface area14170 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9136
Polymers31,6552
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-55 kcal/mol
Surface area14260 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9136
Polymers31,6552
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-10 kcal/mol
Surface area14110 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9136
Polymers31,6552
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-22 kcal/mol
Surface area14050 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0097
Polymers31,6552
Non-polymers3545
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-15 kcal/mol
Surface area14190 Å2
MethodPISA
6
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9136
Polymers31,6552
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-10 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 166.610, 174.980
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
11A
21B
31C
41E
51F
61G
71H
81I
91J
101K
111L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: CU / End label alt-ID: A / End label comp-ID: CU / Refine code: 4 / Auth seq-ID: 3 - 155 / Label seq-ID: 2

Dom-IDAuth asym-IDLabel asym-ID
1AA - M
2BB - O
3CC - S
4EE - W
5FF - Y
6GG - AA
7HH - CA
8II - EA
9JJ - GA
10KK - JA
11LL - LA

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15827.561 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Leishmania tarentolae (eukaryote) / Strain (production host): P10 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) 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.: 3 / Source method: obtained synthetically / Formula: SO4
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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 21-25% (w/v) PEG4000, 0.1 M NaOAc, pH 4.2-5.2, vapor diffusion, hanging drop, temperature 292K
PH range: 4.2-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 28607 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.624 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 11.16
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.5-3.60.5754.3143732306100
3.6-3.70.4635.4124161999100
3.7-3.80.4245.611683187499.9
3.8-3.90.3656.5101191630100
3.9-40.2897.992531485100
4-50.19210.657461926799.9
5-60.15711.9253234128100
6-80.1214.5202713353100
8-100.06722.17169121299.9
10-150.046305378937100
15-300.03935.2189336099.7
30-500.02936.51984795.9
500.04228.925960

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementResolution: 3.5→47.78 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.811 / Occupancy max: 1 / Occupancy min: 1 / SU B: 70.354 / SU ML: 0.491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.692 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1446 5.1 %RANDOM
Rwork0.243 ---
obs0.244 28597 99.96 %-
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 max: 277.39 Å2 / Biso mean: 75.883 Å2 / Biso min: 20.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--4.59 Å20 Å2
3----4.97 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13312 0 39 0 13351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113552
X-RAY DIFFRACTIONr_bond_other_d00.028952
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.94618296
X-RAY DIFFRACTIONr_angle_other_deg4.443322042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28451824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02625.652575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.443152216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6381547
X-RAY DIFFRACTIONr_chiral_restr0.0620.22015
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215631
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022444
X-RAY DIFFRACTIONr_mcbond_it0.1471.58940
X-RAY DIFFRACTIONr_mcbond_other01.53900
X-RAY DIFFRACTIONr_mcangle_it0.27214205
X-RAY DIFFRACTIONr_scbond_it0.36834612
X-RAY DIFFRACTIONr_scangle_it0.6514.54091
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1825 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.030.5
BMEDIUM POSITIONAL0.030.5
CMEDIUM POSITIONAL0.040.5
EMEDIUM POSITIONAL0.040.5
FMEDIUM POSITIONAL0.030.5
GMEDIUM POSITIONAL0.040.5
HMEDIUM POSITIONAL0.040.5
IMEDIUM POSITIONAL0.030.5
JMEDIUM POSITIONAL0.040.5
KMEDIUM POSITIONAL0.040.5
LMEDIUM POSITIONAL0.030.5
AMEDIUM THERMAL0.062
BMEDIUM THERMAL0.082
CMEDIUM THERMAL0.072
EMEDIUM THERMAL0.12
FMEDIUM THERMAL0.072
GMEDIUM THERMAL0.082
HMEDIUM THERMAL0.072
IMEDIUM THERMAL0.062
JMEDIUM THERMAL0.082
KMEDIUM THERMAL0.092
LMEDIUM THERMAL0.062
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 107 -
Rwork0.281 1993 -
all-2100 -
obs--100 %
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)
13.27440.74870.30967.21830.14113.7510.1558-0.0448-0.50220.7686-0.0308-0.24090.49910.1612-0.12510.4139-0.035-0.06670.17810.03030.351424.4313-49.9097-21.191
22.1522-0.91710.40977.2689-0.78533.17110.1215-0.0481-0.16940.1525-0.1554-0.1793-0.11920.18040.03390.0521-0.0983-0.01670.21870.00160.173521.996-23.2487-30.3087
35.97314.10130.56548.26550.86927.41261.3358-0.77360.67711.5519-1.1060.5968-0.5194-0.0183-0.22980.798-0.29730.29610.2997-0.14150.394623.76358.2147-24.7897
42.48990.5688-1.46931.847-1.92312.41080.3452-0.48420.96010.8305-0.09270.1022-0.66180.0694-0.25251.8306-0.72850.5790.7554-0.63730.975329.532929.4846-7.0148
54.82880.6980.8194.875-0.70476.840.14991.74890.5114-0.7859-0.0060.3482-0.5637-0.9815-0.14390.59320.1944-0.13931.93140.18290.37912.15611.1889-81.9817
64.77820.0312-1.37374.062-1.54197.46430.19080.90230.2463-0.1229-0.18870.1255-0.3568-0.0593-0.00210.09420.0973-0.08790.446-0.04720.269917.0676-2.9103-54.3841
71.7988-1.0241-0.54247.1795-0.25085.26680.29910.23180.3372-1.3705-0.29470.4657-0.6551-0.2638-0.00440.96790.2679-0.21160.3148-0.0870.540616.8071-45.7141-58.8609
82.76821.2791-0.60317.85260.48994.0150.20170.0302-0.0697-0.708-0.35970.3328-0.3704-0.10840.1580.29170.132-0.17460.1758-0.12230.274417.8359-72.4777-49.3801
94.39341.10242.05474.40771.47695.13040.06760.2312-0.3905-0.1605-0.0648-0.1320.79520.0384-0.00280.39790.0320.07120.1912-0.12260.390214.1661-126.2632-72.3537
103.3692-0.73870.38154.42762.38235.86250.0318-0.09690.0174-0.06-0.048-0.1752-0.06270.28160.01630.00310.0096-0.01670.1188-0.06820.352816.7888-104.3244-54.604
115.22070.9784-1.38664.283-0.88437.1028-0.0246-1.5516-0.53340.8752-0.2963-0.10150.68450.98140.32090.6855-0.0340.00071.49580.25840.332830.3584-97.90551.6761
124.3295-0.20181.52693.5343-1.21327.66040.1032-0.4247-0.29090.3294-0.25090.10620.15520.31570.14770.1773-0.11990.05190.41-0.05120.261123.1565-93.0065-25.2774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 154
2X-RAY DIFFRACTION2B2 - 154
3X-RAY DIFFRACTION3C2 - 154
4X-RAY DIFFRACTION4D2 - 154
5X-RAY DIFFRACTION5E2 - 154
6X-RAY DIFFRACTION6F2 - 154
7X-RAY DIFFRACTION7G2 - 154
8X-RAY DIFFRACTION8H2 - 154
9X-RAY DIFFRACTION9I2 - 154
10X-RAY DIFFRACTION10J2 - 154
11X-RAY DIFFRACTION11K2 - 154
12X-RAY DIFFRACTION12L2 - 154

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