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- PDB-3kh4: Crystal structure of human Cu/Zn superoxide dismutase recombinant... -

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Basic information

Entry
Database: PDB / ID: 3kh4
TitleCrystal structure of human Cu/Zn superoxide dismutase recombinantly produced in Leishmania tarantolae; P6522 crystal form containing 6 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 / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / myeloid cell homeostasis / regulation of GTPase activity / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / neuronal action potential / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / intracellular iron ion homeostasis / response to ethanol / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / 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 1.2Nov 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,73918
Polymers94,9656
Non-polymers77412
Water00
1
A: Superoxide dismutase [Cu-Zn]
B: 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 area13710 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 area1480 Å2
ΔGint-22 kcal/mol
Surface area13730 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 area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.188, 112.188, 428.268
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15827.561 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
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: 4.1 Å3/Da / Density % sol: 69.97 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→49.69 Å / Num. obs: 21168 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.084 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 13.13
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.5-3.60.5864.2181021668100
3.6-3.70.4954.9160331476100
3.7-3.80.4355.5144521338100
3.8-3.90.3826.3130051212100
3.9-40.2997.7118631100100
4-50.17112.7727066809100
5-60.1514.2321453069100
6-70.11716.7164751607100
7-100.0822.518274182799.9
10-150.04137.96730721100
15-200.02943.71633193100
200.02743.1110214891.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.5→49.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 46.112 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1088 5.1 %RANDOM
Rwork0.201 ---
obs0.201 21168 99.92 %-
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: 157.11 Å2 / Biso mean: 90.385 Å2 / Biso min: 60.37 Å2
Baniso -1Baniso -2Baniso -3
1--8.44 Å2-4.22 Å20 Å2
2---8.44 Å20 Å2
3---12.65 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 12 0 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216774
X-RAY DIFFRACTIONr_bond_other_d00.024482
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9459144
X-RAY DIFFRACTIONr_angle_other_deg4.332311034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16325.625288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.979151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0351524
X-RAY DIFFRACTIONr_chiral_restr0.080.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027818
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021224
X-RAY DIFFRACTIONr_mcbond_it0.4471.54470
X-RAY DIFFRACTIONr_mcbond_other01.51950
X-RAY DIFFRACTIONr_mcangle_it0.93327104
X-RAY DIFFRACTIONr_scbond_it1.40532304
X-RAY DIFFRACTIONr_scangle_it2.634.52040
Refine LS restraints NCS

Ens-ID: 1 / Number: 1857 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.040.05
2BTIGHT POSITIONAL0.040.05
3CTIGHT POSITIONAL0.040.05
4DTIGHT POSITIONAL0.040.05
5ETIGHT POSITIONAL0.040.05
6FTIGHT POSITIONAL0.040.05
1ATIGHT THERMAL0.070.5
2BTIGHT THERMAL0.070.5
3CTIGHT THERMAL0.070.5
4DTIGHT THERMAL0.060.5
5ETIGHT THERMAL0.060.5
6FTIGHT THERMAL0.060.5
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 77 -
Rwork0.257 1451 -
all-1528 -
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)
13.86550.6540.20537.3103-1.41162.6896-0.10680.1620.0159-0.28230.0404-0.08460.1157-0.15770.06640.246-0.01110.08740.20650.06550.0411-13.188-35.383816.2062
23.6428-0.5283-0.39094.93510.53784.59870.0060.25310.4279-0.14490.04940.0679-0.24020.1853-0.05540.2797-0.0360.07470.14060.12880.192-13.72-7.276416.4854
38.0936-2.1316-0.37086.1090.43911.54590.25390.1976-0.2738-0.1149-0.10.2018-0.2134-0.0046-0.15380.32440.03210.02170.37790.13390.29833.1534-62.818216.0965
47.4505-1.38790.2656.2711-0.15273.2117-0.00830.05540.0809-0.0526-0.0107-0.09990.1699-0.05040.0190.25010.0332-0.07120.26070.06430.164727.4514-76.901817.1263
57.99233.31451.0287.29830.61912.2062-0.10120.2566-0.3693-0.2615-0.0246-0.34010.14140.23070.12580.293-0.05480.07430.28620.11090.0931-28.6236-62.994816.558
66.02081.1792-0.22834.7563-0.58612.9501-0.02640.1958-0.404-0.3508-0.0103-0.1362-0.1429-0.11370.03670.2474-0.0572-0.00320.23930.08780.1123-52.8178-77.317217.4908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION2B1 - 153
3X-RAY DIFFRACTION3C1 - 153
4X-RAY DIFFRACTION4D1 - 153
5X-RAY DIFFRACTION5E1 - 153
6X-RAY DIFFRACTION6F1 - 153

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