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- PDB-1o9i: Crystal structure of the Y42F mutant of manganese catalase from L... -

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Basic information

Entry
Database: PDB / ID: 1o9i
TitleCrystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution
ComponentsManganese catalase
KeywordsOXIDOREDUCTASE / HEXAMER / DIMANGANESE CATALASE / METALLOENZYME / PREOXIDASE
Function / homology
Function and homology information


catalase / catalase activity / metal ion binding
Similarity search - Function
manganese catalase, domain 2, chain A / manganese catalase, domain 2, chain A / Manganese catalase, C-terminal / Manganese catalase / Manganese catalase, ferritin-like di-iron-binding domain / Manganese containing catalase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily ...manganese catalase, domain 2, chain A / manganese catalase, domain 2, chain A / Manganese catalase, C-terminal / Manganese catalase / Manganese catalase, ferritin-like di-iron-binding domain / Manganese containing catalase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MANGANESE (III) ION / OXYGEN ATOM / Manganese catalase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsBarynin, V.V. / Whittaker, M.M. / Whittaker, J.W.
Citation
Journal: Eur.J.Biochem. / Year: 2003
Title: Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications.
Authors: Whittaker, M.M. / Barynin, V.V. / Igarashi, T. / Whittaker, J.W.
#1: Journal: Structure / Year: 2001
Title: Crystal Structure of Manganese Catalase from Lactobacillus Plantarum
Authors: Barynin, V.V. / Whittaker, M.M. / Antonyuk, S.V. / Lamzin, V.S. / Harrison, P.M. / Artymiuk, P.J. / Whittaker, J.W.
History
DepositionDec 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry / _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: Manganese catalase
B: Manganese catalase
C: Manganese catalase
D: Manganese catalase
E: Manganese catalase
F: Manganese catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,59837
Polymers178,5806
Non-polymers2,01831
Water26,2841459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.490, 95.270, 105.000
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Manganese catalase / Pseudocatalase


Mass: 29763.379 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Plasmid: PVMG36PSLPA-LPC / Production host: LACTOBACILLUS PLANTARUM (bacteria) / Strain (production host): KAT- L.PLANTARUM (NCDO 1193) / References: UniProt: P60355, catalase

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Non-polymers , 6 types, 1490 molecules

#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1459 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION TYR 42 PHE

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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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, TAPS, PH 8.5, VAPOR DIFFUSION, HANGING DROP AT 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %PEG80001reservoir
20.1 MTAPS1reservoirpH8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 282601 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 14.28 Å2 / Rsym value: 0.041 / Net I/σ(I): 14.9
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 1.88 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.34 / % possible all: 80.7
Reflection
*PLUS
Highest resolution: 1.33 Å / Lowest resolution: 23 Å / Num. obs: 274725 / Redundancy: 2.14 % / Num. measured all: 588079 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 80.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JKV

1jkv


Resolution: 1.33→50 Å / SU B: 2.092 / SU ML: 0.043 / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 14165 5 %RANDOM
Rwork0.115 ---
obs0.117 268292 89.1 %-
Displacement parametersBiso mean: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.36 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12498 0 86 1459 14043
Refinement
*PLUS
Lowest resolution: 48 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.522

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