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- PDB-4bcz: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 4bcz
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form.
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / CU/ZN SOD1 / MONOMERIC MUTANT / DISEASE MUTATION / METAL BINDING / NEURODEGENERATION / ALS
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 / myeloid cell homeostasis / regulation of GTPase activity / 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 / cytosol / cytoplasm
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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSaraboji, K. / Awad, W. / Danielsson, J. / Lang, L. / Kurnik, M. / Marklund, S.L. / Oliveberg, M. / Logan, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Global Structural Motions from the Strain of a Single Hydrogen Bond.
Authors: Danielsson, J. / Awad, W. / Saraboji, K. / Kurnik, M. / Lang, L. / Leinartaite, L. / Marklund, S.L. / Logan, D.T. / Oliveberg, M.
History
DepositionOct 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
B: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)21,9812
Polymers21,9812
Non-polymers00
Water2,648147
1
A: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9901
Polymers10,9901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9901
Polymers10,9901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.430, 74.430, 59.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.338, -0.9408, -0.02539), (-0.9408, -0.3385, 0.01753), (-0.02509, 0.01796, -0.9995)
Vector: -0.4829, 0.4294, -31.93)

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Components

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE 1 / HSOD1


Mass: 10990.290 Da / Num. of mol.: 2 / Fragment: RESIDUES 2049,83-124,141-154 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS C6A, C111A, C146S DELETION OF RESIDUES 49-81 AND 124-139) AND REPLACEMENT BY GAG TRIPEPTIDE LINKERS.

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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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE
Crystal growTemperature: 293 K / Details: 30% PEG 1500, 0.1M MIB BUFFER, PH 4.0, 20 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH 165MM / Detector: CCD / Date: Mar 15, 2011 / Details: HORIZONTALLY FOCUSING MIRROR
RadiationMonochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 14115 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 28.83 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJK

2xjk


Resolution: 1.93→30 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 707 5 %
Rwork0.1693 --
obs0.1718 14115 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 147 1690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081563
X-RAY DIFFRACTIONf_angle_d1.1212111
X-RAY DIFFRACTIONf_dihedral_angle_d12.668543
X-RAY DIFFRACTIONf_chiral_restr0.079245
X-RAY DIFFRACTIONf_plane_restr0.003279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9301-2.07910.28821410.20252669X-RAY DIFFRACTION100
2.0791-2.28830.25731390.19232679X-RAY DIFFRACTION100
2.2883-2.61920.23871460.19192664X-RAY DIFFRACTION100
2.6192-3.29910.27331420.18452690X-RAY DIFFRACTION100
3.2991-28.31690.16891390.14452706X-RAY DIFFRACTION99
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)
13.00081.92620.61554.12230.24494.03150.1178-0.2082-0.37410.3019-0.3031-0.54970.20120.2040.15350.09880.0124-0.03290.17360.10050.214820.5296-18.1824-4.9221
23.42032.9674-0.57074.1187-0.13873.088-0.42270.5057-0.441-0.7590.2489-0.68410.2759-0.0630.07280.2656-0.03220.15520.2081-0.04970.213923.8863-12.9932-28.0034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 1:110)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 2:110)

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