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- PDB-6pm7: The structure of the triclinic crystal form of beef liver catalas... -

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Basic information

Entry
Database: PDB / ID: 6pm7
TitleThe structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution
ComponentsCatalase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / 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 / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMcPherson, A.
CitationJournal: to be published
Title: The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution
Authors: McPherson, A.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7266
Polymers120,0022
Non-polymers2,7244
Water12,755708
1
A: Catalase
B: Catalase
hetero molecules

A: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,45212
Polymers240,0054
Non-polymers5,4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+5/31
Buried area53910 Å2
ΔGint-303 kcal/mol
Surface area58790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.865, 140.865, 101.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 3 - 500 / Label seq-ID: 4 - 501

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Catalase


Mass: 60001.129 Da / Num. of mol.: 2 / Mutation: N213D, N226D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CAT / Production host: Bos taurus (domestic cattle) / References: UniProt: P00432, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Vapor diffusion with 10 ul drops and 0.6 ml reservoirs. Reservoirs were 6% PEG 3350 buffered with 0.1 M MES at pH 6.5. Drops were equal amounts of 35 mg/ml protein in H2O and reservoir ...Details: Vapor diffusion with 10 ul drops and 0.6 ml reservoirs. Reservoirs were 6% PEG 3350 buffered with 0.1 M MES at pH 6.5. Drops were equal amounts of 35 mg/ml protein in H2O and reservoir solution. Growth time about two weeks.
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→122 Å / Num. obs: 97987 / % possible obs: 98.7 % / Redundancy: 17.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.033 / Rrim(I) all: 0.145 / Rsym value: 0.14 / Net I/av σ(I): 9.8 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.9 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 4349 / CC1/2: 0.501 / Rpim(I) all: 1.01 / Rrim(I) all: 2.91 / Rsym value: 2.59 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→121.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.87 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23248 4940 5 %RANDOM
Rwork0.19152 ---
obs0.19363 92909 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.46 Å20 Å2
2---0.91 Å20 Å2
3---2.95 Å2
Refinement stepCycle: 1 / Resolution: 1.85→121.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 182 708 8906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138460
X-RAY DIFFRACTIONr_bond_other_d00.0177388
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.67411538
X-RAY DIFFRACTIONr_angle_other_deg1.2591.58917170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2965994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00921.952502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.571151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.861562
X-RAY DIFFRACTIONr_chiral_restr0.0670.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029622
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021906
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8954.3923982
X-RAY DIFFRACTIONr_mcbond_other3.8934.3913981
X-RAY DIFFRACTIONr_mcangle_it4.7156.5744974
X-RAY DIFFRACTIONr_mcangle_other4.7156.5754975
X-RAY DIFFRACTIONr_scbond_it5.1844.794476
X-RAY DIFFRACTIONr_scbond_other5.1784.7894474
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6517.0366564
X-RAY DIFFRACTIONr_long_range_B_refined8.17385.77236405
X-RAY DIFFRACTIONr_long_range_B_other8.16485.56636073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16188 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 339 -
Rwork0.343 6189 -
obs--90.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59250.2237-0.14950.12120.0570.38930.1087-0.270.27480.0125-0.1180.1297-0.11050.02020.00930.0923-0.02790.01750.1316-0.13880.149-41.109792.9769106.0644
20.40120.1750.04590.15740.07230.21990.0216-0.10350.02370.0252-0.05610.02440.0034-0.07920.03450.0371-0.0160.00450.1153-0.02020.007-58.115463.305299.6399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 558
2X-RAY DIFFRACTION2B3 - 558

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