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- PDB-6po0: The structure of the orthorhombic (P212121) crystal form of beef ... -

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Basic information

Entry
Database: PDB / ID: 6po0
TitleThe structure of the orthorhombic (P212121) 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 / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,45212
Polymers240,0054
Non-polymers5,4488
Water22,9151272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53690 Å2
ΔGint-301 kcal/mol
Surface area58390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.984, 140.386, 228.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 3 - 501 / Label seq-ID: 4 - 502

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Catalase


Mass: 60001.129 Da / Num. of mol.: 4 / Mutation: N213D, N226D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CAT / Production host: Bos taurus (cattle) / References: UniProt: P00432, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 2.8 Å3/Da / Density % sol: 56.11 % / Description: orthorhombic prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grown from 20 mM magnesium formate in 0.1 M Mes pH 6.5 reservoirs with drops equal amounts of 40 mg/ml catalase in water and the reservoir solution. Generally 2 to 6 days at room temperature.
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.75→228.18 Å / Num. obs: 202103 / % possible obs: 74.7 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.033 / Rrim(I) all: 0.156 / Net I/σ(I): 12.6 / Num. measured all: 4257522 / Scaling rejects: 1030
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 6.333 / Num. unique obs: 1168 / CC1/2: 0.062 / Rpim(I) all: 3.52 / Rrim(I) all: 7.314 / % possible all: 8.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.28data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→119.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.741 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 10179 5 %RANDOM
Rwork0.1731 ---
obs0.1748 191814 74.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.48 Å2 / Biso mean: 43.244 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---2.77 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 1.75→119.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16068 0 588 1275 17931
Biso mean--61.77 45.12 -
Num. residues----1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01316976
X-RAY DIFFRACTIONr_bond_other_d00.01714817
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.67423156
X-RAY DIFFRACTIONr_angle_other_deg1.3251.58934444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74551998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01921.9921009
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.281152602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.42515124
X-RAY DIFFRACTIONr_chiral_restr0.0690.22063
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219321
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023819
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16338
12B16338
21A16336
22C16336
31A16352
32D16352
41B16318
42C16318
51B16284
52D16284
61C16239
62D16239
LS refinement shellResolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.496 137 -
Rwork0.476 2254 -
all-2391 -
obs--12.07 %
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)
10.04130.0341-0.00030.75810.09150.07850.0350.05410.0050.30040.03820.06230.01170.0025-0.07320.21350.01280.01770.08190.01460.1554.929438.420387.9622
20.0092-0.0719-0.02140.72530.13990.07670.0277-0.00920.0199-0.19850.0784-0.169-0.06610.0003-0.10610.0977-0.04660.04810.12360.01080.219720.520939.428350.5889
30.0270.0443-0.00180.520.07860.09360.02250.0479-0.02880.01790.0518-0.10560.022-0.0127-0.07430.05050.0139-0.06830.1201-0.0390.244420.86315.555157.6321
40.01840.01960.01250.89750.31010.2629-0.01630.01840.03250.4430.2466-0.47460.10350.0363-0.23040.27930.1112-0.28410.0925-0.06870.399134.684321.342192.2657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 1102
2X-RAY DIFFRACTION2B3 - 1202
3X-RAY DIFFRACTION3C3 - 1302
4X-RAY DIFFRACTION4D3 - 1402

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