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- PDB-4ff9: Crystal Structure of cysteinylated WT SOD1. -

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Basic information

Entry
Database: PDB / ID: 4ff9
TitleCrystal Structure of cysteinylated WT SOD1.
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / superoxide dismutase / zinc binding / cysteinylation
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / regulation of organ growth / protein phosphatase 2B binding / dense core granule / anterograde axonal transport / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / regulation of organ growth / protein phosphatase 2B binding / dense core granule / anterograde axonal transport / response to superoxide / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / Oxidoreductases; Acting on a sulfur group of donors / regulation of GTPase activity / retina homeostasis / auditory receptor cell stereocilium organization / cellular response to potassium ion / hydrogen peroxide biosynthetic process / retrograde axonal transport / myeloid cell homeostasis / superoxide anion generation / superoxide metabolic process / response to copper ion / superoxide dismutase / muscle cell cellular homeostasis / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / heart contraction / cellular response to ATP / cellular response to cadmium ion / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / ovarian follicle development / neuronal action potential / positive regulation of superoxide anion generation / axon cytoplasm / removal of superoxide radicals / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / dendrite cytoplasm / placenta development / thymus development / positive regulation of cytokine production / determination of adult lifespan / response to amphetamine / regulation of mitochondrial membrane potential / glutathione metabolic process / response to hydrogen peroxide / locomotory behavior / sensory perception of sound / response to nutrient levels / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / lysosome / positive regulation of apoptotic process / response to xenobiotic stimulus / mitochondrial matrix / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / 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 / CYSTEINE / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5003 Å
AuthorsAuclair, J.R. / Brodkin, H.R. / D'Aquino, J.A. / Ringe, D. / Petsko, G.A. / Agar, J.N.
CitationJournal: Biochemistry / Year: 2013
Title: Structural consequences of cysteinylation of cu/zn-superoxide dismutase.
Authors: Auclair, J.R. / Brodkin, H.R. / D'Aquino, J.A. / Petsko, G.A. / Ringe, D. / Agar, J.N.
History
DepositionMay 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 13, 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_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 27, 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0347
Polymers31,6552
Non-polymers3795
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-15 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.050, 113.050, 70.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 15827.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEp-351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EGy118(delta SOD1) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.11 Å3/Da / Density % sol: 70.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 0.1M MES, pH 6.25, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.48→27.154 Å / Num. obs: 16978 / % possible obs: 94.75 % / Observed criterion σ(F): 0.11 / Observed criterion σ(I): 2
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1831 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPD

1spd


Resolution: 2.5003→27.154 Å / SU ML: 1.04 / σ(F): 0.11 / Phase error: 37.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3351 1688 9.94 %RANDOM
Rwork0.2762 ---
obs0.2822 16978 94.75 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.883 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5434 Å20 Å20 Å2
2---1.5434 Å2-0 Å2
3---3.0868 Å2
Refinement stepCycle: LAST / Resolution: 2.5003→27.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 10 24 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092233
X-RAY DIFFRACTIONf_angle_d1.2543020
X-RAY DIFFRACTIONf_dihedral_angle_d16.26784
X-RAY DIFFRACTIONf_chiral_restr0.085337
X-RAY DIFFRACTIONf_plane_restr0.004412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.57380.37711150.34411056X-RAY DIFFRACTION79
2.5738-2.65680.37591380.32161205X-RAY DIFFRACTION90
2.6568-2.75170.44541400.32211197X-RAY DIFFRACTION91
2.7517-2.86170.40361390.32421236X-RAY DIFFRACTION93
2.8617-2.99180.36951420.30771268X-RAY DIFFRACTION95
2.9918-3.14930.33571460.27791301X-RAY DIFFRACTION97
3.1493-3.34630.38821420.28491334X-RAY DIFFRACTION98
3.3463-3.60410.30871450.28931312X-RAY DIFFRACTION98
3.6041-3.96580.35721390.26661323X-RAY DIFFRACTION99
3.9658-4.53740.30361470.24951351X-RAY DIFFRACTION99
4.5374-5.70790.29061420.24541353X-RAY DIFFRACTION100
5.7079-27.15530.30631530.26671354X-RAY DIFFRACTION98
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)
15.3849-2.0374-4.5650.77371.72843.8704-2.8483-5.9368-1.05712.22852.41940.84181.17490.73780.45730.77790.2232-0.18891.67220.27781.1081-28.900315.6388-21.9263
20.1138-0.2169-0.03970.41260.07470.013-0.45070.29790.73460.02160.38540.2451-0.11840.0082-0.01780.46240.0971-0.13240.44030.16570.3034-20.421716.7938-3.9602
30.3795-0.0542-0.28910.44250.00140.22380.07260.39860.2172-0.46790.0835-0.0211-0.2901-0.1348-0.05240.495-0.25320.09340.44580.28370.247-15.643819.6111-17.7818
41.0577-0.2075-0.3410.37130.32190.31290.0590.1880.2523-0.21040.15320.1207-0.01610.13550.51120.27120.00650.09860.18460.2375-0.0802-11.954512.2317-5.9837
50.00260.0418-0.00551.49070.2320.3037-0.30570.29210.19660.06770.19920.5925-0.3066-0.2422-0.29630.22780.0019-0.05390.25230.20640.4407-26.7935.3209-8.8757
60.7045-0.3702-0.08590.6170.35550.2401-0.11550.69040.1552-0.81340.16230.31370.1195-0.3349-0.27090.33170.0399-0.13540.36330.1062-0.1222-14.47460.2822-19.2058
71.30580.4380.54930.49010.16720.232-0.06190.572-0.0842-0.59270.087-0.05970.31740.18320.27750.2731-0.06550.05460.43-0.0005-0.128-12.82112.6676-18.1469
80.5716-0.29970.20120.1538-0.10260.06830.0715-0.39530.04850.431-0.0827-0.0638-0.11820.2224-0.16320.34470.0736-0.03060.31070.0177-0.0106-5.919213.06780.4037
91.0090.7938-0.41040.638-0.33050.17350.09030.55430.4174-0.21080.1730.3104-0.0386-0.11190.33440.2290.1554-0.11860.27690.4485-0.3328-14.91958.13-12.8518
100.49280.23580.07070.10860.03330.28120.00630.39090.2893-0.32260.08980.48690.02450.1950.17620.24440.0234-0.07460.26940.24650.3553-18.88264.8319-7.7563
110.6787-0.0843-0.22310.214-0.1110.40720.17380.15960.5899-0.0422-0.0330.0203-0.1747-0.11090.25830.19740.124-0.12790.30550.21850.9248-37.241314.4416-5.826
120.7774-0.2542-0.09930.21220.02140.65860.23240.5441-0.1873-0.2484-0.2563-0.0326-0.09-0.26970.0190.2080.1712-0.01880.3742-0.09610.8368-44.42915.6755-9.8663
131.4272-0.2698-0.1750.8325-0.1390.1565-0.1006-0.09330.170.17230.2011-0.0015-0.0658-0.0714-0.41330.16170.16620.13620.42380.32690.8595-35.000525.6814-7.1835
140.06810.12770.01560.23630.02820.00280.03820.09820.1402-0.01880.18730.55070.267-0.2590.06090.4228-0.0335-0.07180.38110.39090.887-37.884330.4691-14.8877
150.50780.61370.24920.89970.6981.1982-0.45150.2405-0.47640.18850.11130.1777-0.7709-0.62860.0640.40380.25650.03190.52810.20370.8797-46.949125.3512-9.0221
160.13320.1613-0.00280.25120.09430.17760.26570.2208-0.3354-0.15270.17630.26420.0637-0.18910.00540.34550.082-0.06450.42490.14110.891-46.66218.1845-13.3816
170.8540.69150.24760.56890.25660.53710.55830.62880.3078-0.542-0.26610.4352-0.0892-0.39160.03790.57050.2786-0.11370.43990.15880.7671-35.282821.0906-15.3401
180.4308-0.19090.02341.36730.9490.696-0.09520.18110.7719-0.2851-0.14930.3841-0.4943-0.068-0.30450.3872-0.0467-0.01620.37420.26931.2508-40.586329.9535-7.193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 201
2X-RAY DIFFRACTION2chain 'A' and (resseq 1:15)
3X-RAY DIFFRACTION3chain 'A' and (resseq 16:28)
4X-RAY DIFFRACTION4chain 'A' and (resseq 29:48)
5X-RAY DIFFRACTION5chain 'A' and (resseq 49:65)
6X-RAY DIFFRACTION6chain 'A' and (resseq 66:75)
7X-RAY DIFFRACTION7chain 'A' and (resseq 76:85)
8X-RAY DIFFRACTION8chain 'A' and (resseq 86:94)
9X-RAY DIFFRACTION9chain 'A' and (resseq 95:131)
10X-RAY DIFFRACTION10chain 'A' and (resseq 132:153)
11X-RAY DIFFRACTION11chain 'B' and (resseq 1:21)
12X-RAY DIFFRACTION12chain 'B' and (resseq 22:40)
13X-RAY DIFFRACTION13chain 'B' and (resseq 41:56)
14X-RAY DIFFRACTION14chain 'B' and (resseq 57:75)
15X-RAY DIFFRACTION15chain 'B' and (resseq 76:94)
16X-RAY DIFFRACTION16chain 'B' and (resseq 95:104)
17X-RAY DIFFRACTION17chain 'B' and (resseq 105:120)
18X-RAY DIFFRACTION18chain 'B' and (resseq 121:153)

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