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- PDB-1luw: CATALYTIC AND STRUCTURAL EFFECTS OF AMINO-ACID SUBSTITUTION AT HI... -

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Entry
Database: PDB / ID: 1luw
TitleCATALYTIC AND STRUCTURAL EFFECTS OF AMINO-ACID SUBSTITUTION AT HIS 30 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE: INSERTION OF VAL CGAMMA INTO THE SUBSTRATE ACCESS CHANNEL
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE / Human Manganese superoxide dismutase / MnSOD
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / intracellular oxygen homeostasis / response to L-ascorbic acid ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / intracellular oxygen homeostasis / response to L-ascorbic acid / response to selenium ion / response to superoxide / response to manganese ion / hydrogen peroxide biosynthetic process / superoxide anion generation / intrinsic apoptotic signaling pathway in response to oxidative stress / response to zinc ion / positive regulation of vascular associated smooth muscle cell apoptotic process / superoxide metabolic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to isolation stress / superoxide dismutase / negative regulation of fat cell differentiation / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / response to immobilization stress / cellular response to ethanol / hemopoiesis / negative regulation of vascular associated smooth muscle cell proliferation / mitochondrial nucleoid / response to electrical stimulus / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / response to cadmium ion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / neuron development / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / response to activity / response to gamma radiation / post-embryonic development / regulation of mitochondrial membrane potential / respiratory electron transport chain / locomotory behavior / response to hydrogen peroxide / liver development / Transcriptional activation of mitochondrial biogenesis / oxygen binding / multicellular organismal-level iron ion homeostasis / regulation of blood pressure / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / manganese ion binding / heart development / cellular response to oxidative stress / response to lipopolysaccharide / protein homotetramerization / negative regulation of neuron apoptotic process / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHearn, A.S. / Stroupe, M.E. / Ramilo, C.A. / Luba, J.P. / Cabelli, D.E. / Tainer, J.A. / Silverman, D.N.
CitationJournal: Biochemistry / Year: 2003
Title: Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel
Authors: Hearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Ramilo, C.A. / Luba, J.P. / Tainer, J.A. / Nick, H.S. / Silverman, D.N.
History
DepositionMay 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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_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_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 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7486
Polymers44,4462
Non-polymers3024
Water3,513195
1
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules

A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49612
Polymers88,8924
Non-polymers6048
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area8490 Å2
ΔGint-83 kcal/mol
Surface area31660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.364, 79.364, 242.576
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
11A-339-

HOH

DetailsThe asymmetric unit contains a dimer; to generate the active tetramer apply the following rotation and translation to chains A and B 0.500000 -0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 -1.00000 translation: 39.82150 68.97286 201.36833

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Components

#1: Protein Superoxide dismutase [Mn]


Mass: 22223.094 Da / Num. of mol.: 2 / Mutation: H30Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHMNSOD4 / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 (SOD--) / References: UniProt: P04179, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM imidazole/malate, 2.5 M ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: unknown / PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-3 Mammonium sulfate11pH7-8
2100 mMimidazole malate11

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Data collection

DiffractionMean temperature: 272 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 31, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→17 Å / Num. obs: 19640 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.06 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.075 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.45 % / Mean I/σ(I) obs: 2.55 / Num. unique all: 648 / Rsym value: 0.334 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 17 Å / % possible obs: 93 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: hMnSOD Y34F

Resolution: 2.3→16.81 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1932 9.8 %RANDOM
Rwork0.239 ---
obs0.239 19618 93.5 %-
all-19640 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4849 Å2 / ksol: 0.345009 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å24.1 Å20 Å2
2--2.9 Å20 Å2
3----5.79 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→16.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 12 195 3351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 291 9.3 %
Rwork0.28 2845 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 17 Å / % reflection Rfree: 9 % / Rfactor obs: 0.234 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rwork: 0.28 / Rfactor obs: 0.28

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