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- PDB-1ja8: Kinetic Analysis of Product Inhibition in Human Manganese Superox... -

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Basic information

Entry
Database: PDB / ID: 1ja8
TitleKinetic Analysis of Product Inhibition in Human Manganese Superoxide Dismutase
ComponentsManganese Superoxide Dismutase
KeywordsOXIDOREDUCTASE / manganese / superoxide / disumtase / SOD / MnSOD / homo sapien / alpha-beta / two-domain / homotetramer / hydrogen bond network
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsHearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Lepock, J.R. / Tainer, J.A. / Nick, H.S. / Silverman, D.S.
CitationJournal: Biochemistry / Year: 2001
Title: Kinetic analysis of product inhibition in human manganese superoxide dismutase.
Authors: Hearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Lepock, J.R. / Tainer, J.A. / Nick, H.S. / Silverman, D.N.
History
DepositionMay 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: 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 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)44,7308
Polymers44,2362
Non-polymers4946
Water6,449358
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)89,46016
Polymers88,4724
Non-polymers98812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area10150 Å2
ΔGint-168 kcal/mol
Surface area31360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.608, 79.608, 240.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Manganese Superoxide Dismutase / SUPEROXIDE DISMUTASE [MN] / MITOCHONDRIAL


Mass: 22117.980 Da / Num. of mol.: 2 / Mutation: W161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHMNSDO4 / Production host: Escherichia coli (E. coli) / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 50.45 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8
Details: ammonium sulfate, imidazole-malate, pH 8, VAPOR DIFFUSION, temperature 300K
Crystal grow
*PLUS
Method: unknown / PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-3 Mammonium sulfate11
2100 mMimidazole malate11

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Data collection

DiffractionMean temperature: 132 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 2000
RadiationMonochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.773 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 27115 / Num. obs: 26963 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AP6

1ap6


Resolution: 2.12→17.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4108688.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2591 9.9 %RANDOM
Rwork0.243 ---
all-26963 --
obs-26963 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.35 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å24.74 Å20 Å2
2--2.64 Å20 Å2
3----5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.12→17.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 22 358 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.221.5
X-RAY DIFFRACTIONc_mcangle_it0.422
X-RAY DIFFRACTIONc_scbond_it0.142
X-RAY DIFFRACTIONc_scangle_it0.252.5
LS refinement shellResolution: 2.12→2.25 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 438 10.2 %
Rwork0.313 3867 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it0.221.5
X-RAY DIFFRACTIONc_scbond_it0.142
X-RAY DIFFRACTIONc_mcangle_it0.422
X-RAY DIFFRACTIONc_scangle_it0.252.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.356 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.313

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