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- PDB-2v8t: Crystal structure of Mn catalase from Thermus Thermophilus comple... -

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Basic information

Entry
Database: PDB / ID: 2v8t
TitleCrystal structure of Mn catalase from Thermus Thermophilus complexed with chloride
ComponentsMANGANESE-CONTAINING PSEUDOCATALASE
KeywordsOXIDOREDUCTASE / MANGANESE CATALASE
Function / homology
Function and homology information


catalase / catalase activity / metal ion binding
Similarity search - Function
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 / Mainly Alpha
Similarity search - Domain/homology
: / : / Pseudocatalase / Manganese catalase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsAntonyuk, S.V. / Barynin, V.V. / Vaguine, A.A. / Melik-Adamyan, W.R. / Popov, A.N. / Lamsin, V.S. / Harrison, P.M. / Artymiuk, P.J.
CitationJournal: Crystallogr.Rep.(Transl. Kristallografiya) / Year: 2000
Title: Three-Dimentional Structure of the Enzyme Dimanganese Catalase from Thermus Thermophilus at 1 Angstrom Resolution
Authors: Antonyuk, S.V. / Melik-Adamyan, W.R. / Popov, A.N. / Lamsin, V.S. / Hempstead, P.D. / Harrison, P.M. / Artymyuk, P.J. / Barynin, V.V.
History
DepositionAug 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE-CONTAINING PSEUDOCATALASE
B: MANGANESE-CONTAINING PSEUDOCATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,63517
Polymers66,6902
Non-polymers94515
Water17,997999
1
A: MANGANESE-CONTAINING PSEUDOCATALASE
B: MANGANESE-CONTAINING PSEUDOCATALASE
hetero molecules

A: MANGANESE-CONTAINING PSEUDOCATALASE
B: MANGANESE-CONTAINING PSEUDOCATALASE
hetero molecules

A: MANGANESE-CONTAINING PSEUDOCATALASE
B: MANGANESE-CONTAINING PSEUDOCATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,90551
Polymers200,0716
Non-polymers2,83545
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48340 Å2
ΔGint-356.3 kcal/mol
Surface area60080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.070, 132.070, 132.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-1304-

SO4

21B-1304-

SO4

31A-2091-

HOH

41A-2178-

HOH

51A-2180-

HOH

61B-2095-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MANGANESE-CONTAINING PSEUDOCATALASE / DIMANGANESE CATALASE


Mass: 33345.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / References: UniProt: Q84DB4, UniProt: Q72GH6*PLUS, catalase

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Non-polymers , 5 types, 1014 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.99 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.98→30 Å / Num. obs: 413309 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30
Reflection shellResolution: 0.98→0.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8U

2v8u


Resolution: 0.98→30 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.341 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.117 866 0.2 %RANDOM
Rwork0.101 ---
obs0.101 424276 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.11 Å2
Refinement stepCycle: LAST / Resolution: 0.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 39 999 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225197
X-RAY DIFFRACTIONr_bond_other_d0.0020.023620
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9817054
X-RAY DIFFRACTIONr_angle_other_deg1.84538900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76224.51255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28515958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8291530
X-RAY DIFFRACTIONr_chiral_restr0.1350.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025650
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021004
X-RAY DIFFRACTIONr_nbd_refined0.2880.21335
X-RAY DIFFRACTIONr_nbd_other0.2140.24032
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22523
X-RAY DIFFRACTIONr_nbtor_other0.0970.22410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3170.2734
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5550.272
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4020.2144
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5220.2173
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1531.54012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49125052
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.81432427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7054.51997
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.98→1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 54
Rwork0.203 29408

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