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- PDB-1em1: X-RAY CRYSTAL STRUCTURE FOR HUMAN MANGANESE SUPEROXIDE DISMUTASE,... -

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Entry
Database: PDB / ID: 1em1
TitleX-RAY CRYSTAL STRUCTURE FOR HUMAN MANGANESE SUPEROXIDE DISMUTASE, Q143A
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / alpha-beta protein / metalloenzyme
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of membrane hyperpolarization / : / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to selenium ion / response to L-ascorbic acid / intracellular oxygen homeostasis / response to superoxide ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of membrane hyperpolarization / : / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to selenium ion / response to L-ascorbic acid / intracellular oxygen homeostasis / response to superoxide / response to manganese ion / hydrogen peroxide biosynthetic process / response to zinc ion / superoxide metabolic process / positive regulation of vascular associated smooth muscle cell apoptotic process / superoxide dismutase / Detoxification of Reactive Oxygen Species / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide dismutase activity / response to immobilization stress / response to isolation stress / negative regulation of vascular associated smooth muscle cell proliferation / mitochondrial nucleoid / response to cadmium ion / response to electrical stimulus / cellular response to ethanol / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Mitochondrial unfolded protein response (UPRmt) / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to activity / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / oxygen binding / regulation of blood pressure / manganese ion binding / negative regulation of neuron apoptotic process / response to lipopolysaccharide / cellular response to oxidative stress / response to hypoxia / protein homotetramerization / response to xenobiotic stimulus / positive regulation of cell migration / mitochondrial matrix / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding
Similarity search - Function
: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain ...: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.13 Å
AuthorsLeveque, V. / Stroupe, M.E. / Lepock, J.R. / Cabelli, D.E. / Tainer, J.A. / Nick, H.S. / Silverman, D.N.
Citation
Journal: Biochemistry / Year: 2000
Title: Multiple replacements of glutamine 143 in human manganese superoxide dismutase: effects on structure, stability, and catalysis.
Authors: Leveque, V.J. / Stroupe, M.E. / Lepock, J.R. / Cabelli, D.E. / Tainer, J.A. / Nick, H.S. / Silverman, D.N.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The Structure of Human Mitochondrial Manganese Superoxide Dismutase Reveals a Novel Tetrameric Interface of Two 4-Helix Bundles
Authors: Borgstahl, G.E. / Parge, H.E. / Hickey, M.J. / Beyer Junior, W.F. / Hallewell, R.A. / Tainer, J.A.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6546
Polymers44,3522
Non-polymers3024
Water5,278293
1
A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules

A: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,30812
Polymers88,7044
Non-polymers6048
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area9160 Å2
ΔGint-95 kcal/mol
Surface area31670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.643, 79.643, 241.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-691-

HOH

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Components

#1: Protein MANGANESE SUPEROXIDE DISMUTASE / HMNSOD


Mass: 22176.061 Da / Num. of mol.: 2 / Mutation: Q143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organelle: MITOCHONDRIA / Production host: Escherichia coli (E. coli) / Strain (production host): SODASODB / References: UniProt: P04179, superoxide dismutase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, imidazole/malate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0-2.8 Mammonium sulfate1drop
2100 mMimidazole malate1drop
320 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 89153 / Num. obs: 89153 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.7
Reflection shellResolution: 2.12→2.2 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.33 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 26135 / Num. measured all: 89153

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.13→19.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3778026.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2574 9.8 %RANDOM
Rwork0.232 ---
all0.232 ---
obs0.232 89153 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.94 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.26 Å25.15 Å20 Å2
2--4.26 Å20 Å2
3----8.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.13→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 12 293 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it0.251.5
X-RAY DIFFRACTIONc_mcangle_it0.472
X-RAY DIFFRACTIONc_scbond_it0.192
X-RAY DIFFRACTIONc_scangle_it0.332.5
LS refinement shellResolution: 2.12→2.25 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 390 9.7 %
Rwork0.256 3625 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ALL.PARAMALL2.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 26135 / σ(F): 1 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.301 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.256

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