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- PDB-4bd4: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 4bd4
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, mutant H43F
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 / 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsAwad, W. / Saraboji, K. / 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 4, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,36213
Polymers98,9949
Non-polymers3684
Water95553
1
A: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0912
Polymers10,9991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0912
Polymers10,9991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9991
Polymers10,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9991
Polymers10,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9991
Polymers10,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9991
Polymers10,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0912
Polymers10,9991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0912
Polymers10,9991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: SUPEROXIDE DISMUTASE [CU-ZN]


Theoretical massNumber of molelcules
Total (without water)10,9991
Polymers10,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)235.030, 49.890, 97.940
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9345, 0.3547, -0.02911), (-0.3548, -0.9349, -0.001732), (-0.02783, 0.008711, 0.9996)-54.38, -36.29, -24.33
2given(-0.957, -0.2826, -0.06546), (0.284, -0.9587, -0.01324), (-0.05902, -0.03127, 0.9978)-63.57, -16.75, 21.43
3given(0.6903, -0.7234, -0.01316), (0.7226, 0.6882, 0.06522), (-0.03812, -0.05453, 0.9978)-17.65, 16.22, -48.97
4given(0.692, 0.7156, 0.09518), (0.7138, -0.6979, 0.05798), (0.1079, 0.02782, -0.9938)-11.92, 21, 49.43
5given(-0.4047, -0.9106, -0.08344), (-0.9112, 0.4093, -0.0467), (0.07668, 0.05713, -0.9954)-36.32, -52.49, 25.34
6given(-0.9029, -0.4271, -0.04784), (-0.4273, 0.9041, -0.008338), (0.04681, 0.01291, -0.9988)-62.27, -38.32, 71.37
7given(0.04069, -0.9989, -0.02236), (0.9975, 0.0393, 0.05946), (-0.05852, -0.02472, 0.998)-76.3, 0.1659, -0.3285
8given(0.9847, 0.1691, 0.04292), (0.1701, -0.9852, -0.02175), (0.03861, 0.02872, -0.9988)2.147, -44.16, 95.02

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Components

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


Mass: 10999.317 Da / Num. of mol.: 9 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS C6A, H43F, F50E, G51E, C111A, DELETION OF RESIDUES 49-81 AND 124-139) AND REPLACEMENT BY ...MUTATIONS C6A, H43F, F50E, G51E, C111A, 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: 3.01 Å3/Da / Density % sol: 51.15 % / Description: NONE
Crystal growDetails: 18 % PEG 1500, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0409
DetectorType: MARRESEARCH 165MM / Detector: CCD / Date: May 18, 2012 / Details: HORIZONTALLY FOCUSING MIRROR
RadiationMonochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0409 Å / Relative weight: 1
ReflectionResolution: 2.78→30 Å / Num. obs: 28537 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 69.56 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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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: 2.78→29.148 Å / SU ML: 0.39 / σ(F): 2 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1437 5.1 %
Rwork0.1802 --
obs0.1837 28343 98.12 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 85.4 Å2
Refinement stepCycle: LAST / Resolution: 2.78→29.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6687 0 24 53 6764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086789
X-RAY DIFFRACTIONf_angle_d1.2849148
X-RAY DIFFRACTIONf_dihedral_angle_d14.7512351
X-RAY DIFFRACTIONf_chiral_restr0.0871075
X-RAY DIFFRACTIONf_plane_restr0.0051184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7801-2.87940.37011540.31322664X-RAY DIFFRACTION99
2.8794-2.99460.34081460.27932669X-RAY DIFFRACTION99
2.9946-3.13070.30541330.24612720X-RAY DIFFRACTION99
3.1307-3.29550.28941360.22522699X-RAY DIFFRACTION99
3.2955-3.50170.30461300.20072699X-RAY DIFFRACTION99
3.5017-3.77150.24671420.18512696X-RAY DIFFRACTION99
3.7715-4.15010.23181470.16832688X-RAY DIFFRACTION98
4.1501-4.74840.20441400.14372675X-RAY DIFFRACTION98
4.7484-5.9740.23031550.15752676X-RAY DIFFRACTION97
5.974-29.14960.21971540.15782720X-RAY DIFFRACTION95
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)
15.757-0.54960.22414.8138-1.36285.9750.2581-0.3591-0.37390.1153-0.3327-0.0798-0.33780.33020.08210.4728-0.13480.01170.7946-0.07030.3119-36.2879-13.001926.9881
25.11930.8037-1.16926.4971-1.16067.7776-0.14880.10430.3042-0.14390.0027-0.03350.2238-0.02030.070.4102-0.07150.05250.5245-0.08810.2906-25.8662-11.27423.5935
38.92860.0183.0435.01350.12945.6086-0.5637-0.51490.32380.61240.0728-0.3327-0.98940.9910.47940.8139-0.2028-0.13811.0314-0.00110.4417-27.0311-14.97950.8909
44.59470.98720.53436.6011.08673.67030.09430.13730.25440.06310.0210.1582-0.3126-0.1548-0.15730.6508-0.27260.07361.1975-0.00050.3794-33.6596-17.5803-19.7274
57.2860.1806-0.64648.83391.05437.65910.16540.74890.7477-0.5275-0.0125-0.5599-0.43540.43-0.05510.44610.06930.08770.8420.0420.4686-44.2115.608918.22
68.1676-0.2436-0.06643.6627-1.54464.7414-0.08240.5033-0.6767-0.69110.1082-0.12360.91370.29910.0040.6768-0.07170.15160.7809-0.16350.5392-11.5849-25.8117-5.5004
77.28990.6874-1.5464.8552-1.00443.1338-0.12080.2666-0.7168-0.3218-0.1276-0.38831.14051.90710.25630.83060.3487-0.02191.3887-0.17320.5586-25.4159-34.796742.5986
87.69363.1072-0.97098.1051-0.78795.64120.4024-0.03580.79870.5241-0.27010.2658-0.9682-0.0964-0.11480.6630.22250.13490.9142-0.05440.6008-64.6561-35.933229.5308
98.7227-0.6898-1.94348.10090.02368.8884-0.1979-0.2471-0.6235-0.04-0.2756-0.14481.85260.65920.46340.9296-0.05850.06550.98780.09720.4514-35.0878-37.588965.648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 1:109)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 1:109)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 2:109)
4X-RAY DIFFRACTION4(CHAIN D AND RESSEQ 1:109)
5X-RAY DIFFRACTION5(CHAIN E AND RESSEQ 1:109)
6X-RAY DIFFRACTION6(CHAIN F AND RESSEQ 1:109)
7X-RAY DIFFRACTION7(CHAIN G AND RESSEQ 2:109)
8X-RAY DIFFRACTION8(CHAIN H AND RESSEQ 1:110)
9X-RAY DIFFRACTION9(CHAIN I AND RESSEQ 1:109)

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