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- PDB-6pt7: Structure of KatE1 catalase from Acinetobacter sp. Ver3 -

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Basic information

Entry
Database: PDB / ID: 6pt7
TitleStructure of KatE1 catalase from Acinetobacter sp. Ver3
ComponentsCatalase
KeywordsOXIDOREDUCTASE / catalase / peroxide / NADP / cold-adapted
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / nucleotide binding / heme binding / metal ion binding
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Catalase
Similarity search - Component
Biological speciesAcinetobacter sp. Ver3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGonzalez, J.M. / Sartorio, M.G. / Cortez, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina
Authors: Sartorio, M.G. / Cortez, N. / Gonzalez, J.M.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1577
Polymers56,7611
Non-polymers1,3956
Water4,270237
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,62628
Polymers227,0454
Non-polymers5,58124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area51690 Å2
ΔGint-233 kcal/mol
Surface area56900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.538, 112.538, 314.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-733-

HOH

21A-759-

HOH

31A-903-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catalase


Mass: 56761.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. Ver3 (bacteria) / Gene: CL42_01515 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A031LXI5

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium HEPES pH 7.5, 0.8 M Na-K tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.15→49.75 Å / Num. obs: 55226 / % possible obs: 99.82 % / Redundancy: 14.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1783 / Net I/σ(I): 11.32
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 5401 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISA

2isa


Resolution: 2.15→49.75 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.422 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 2662 4.8 %RANDOM
Rwork0.1742 ---
obs0.1758 52559 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.65 Å2 / Biso mean: 49.741 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20 Å2
2--3.38 Å20 Å2
3----6.77 Å2
Refinement stepCycle: final / Resolution: 2.15→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 95 239 4339
Biso mean--57.01 50.66 -
Num. residues----500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173691
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.6915759
X-RAY DIFFRACTIONr_angle_other_deg1.3741.68560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4495501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52222.101257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49215647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571533
X-RAY DIFFRACTIONr_chiral_restr0.080.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024836
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02971
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 203 -
Rwork0.383 3807 -
all-4010 -
obs--99.68 %

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