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- PDB-1jkv: Crystal Structure of Manganese Catalase from Lactobacillus planta... -

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Basic information

Entry
Database: PDB / ID: 1jkv
TitleCrystal Structure of Manganese Catalase from Lactobacillus plantarum complexed with azide
Componentspseudocatalase
KeywordsOXIDOREDUCTASE / hexamer / catalase dimanganese / metalloenzyme
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
AZIDE ION / MANGANESE (III) ION / HYDROXIDE ION / Manganese catalase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsBarynin, V.V. / Whittaker, M.M. / Antonyuk, S.V. / Lamzin, V.S. / Harrison, P.M. / Artymiuk, P.J. / Whittaker, J.W.
CitationJournal: 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
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Aug 16, 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_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_asym_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_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: pseudocatalase
B: pseudocatalase
C: pseudocatalase
D: pseudocatalase
E: pseudocatalase
F: pseudocatalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,06563
Polymers178,6766
Non-polymers2,38957
Water27,6351534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66810 Å2
ΔGint-455 kcal/mol
Surface area41150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.210, 95.550, 106.110
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
pseudocatalase / E.C.1.11.1.6 / MANGANESE-CONTAINING CATALASE /


Mass: 29779.379 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Lactobacillus plantarum (bacteria) / Strain: ATCC 14431 / References: UniProt: P60355, catalase

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Non-polymers , 6 types, 1591 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#5: Chemical
ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1534 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 8000, TAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K, pH 8.7
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
225 %PEG80001reservoir
30.1 MTAPS1reservoirpH8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.811 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.39→17 Å / Num. all: 269006 / Num. obs: 269006 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Rsym value: 5 / Net I/σ(I): 16.4
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.1 / Num. unique all: 15234 / Rsym value: 14 / % possible all: 78.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 663270 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å / % possible obs: 78.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.13

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Processing

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

1jku


Resolution: 1.39→17 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.12961 13879 5.1 %RANDOM
Rwork0.10379 ---
all0.1037 260556 --
obs0.10509 260556 97.24 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.975 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: 1.39→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12504 0 114 1534 14152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.014012912
X-RAY DIFFRACTIONp_angle_d1.5451.917348
X-RAY DIFFRACTIONp_mcbond_it1.3541.57928
X-RAY DIFFRACTIONp_mcangle_it1.959212679
X-RAY DIFFRACTIONp_scbond_it3.1134984
X-RAY DIFFRACTIONp_scangle_it4.5314.54669
LS refinement shellResolution: 1.39→1.43 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 860 -
Rwork0.119 --
obs-15234 77.8 %
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 17 Å / Num. reflection Rfree: 13288 / % reflection Rfree: 5 % / Rfactor all: 0.1037 / Rfactor obs: 0.10509 / Rfactor Rfree: 0.13 / Rfactor Rwork: 0.104
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg21.54
LS refinement shell
*PLUS
Rfactor Rfree: 0.172 / Rfactor Rwork: 0.119

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