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- PDB-3nwl: The crystal structure of the P212121 form of bovine liver catalas... -

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Basic information

Entry
Database: PDB / ID: 3nwl
TitleThe crystal structure of the P212121 form of bovine liver catalase previously characterized by electron microscopy
ComponentsCatalase
KeywordsOXIDOREDUCTASE / oxioreductase / NADPH / HEME b
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 / Resolution: 2.69 Å
AuthorsForoughi, L.M. / Kang, Y.N. / Matzger, A.J.
CitationJournal: Cryst.Growth Des. / Year: 2011
Title: Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms
Authors: Foroughi, L.M. / Kang, Y.N. / Matzger, A.J.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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_ref_seq_dif / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,45212
Polymers240,0054
Non-polymers5,4488
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53810 Å2
ΔGint-300 kcal/mol
Surface area61160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.652, 173.744, 186.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 501
2111B1 - 501
3111C1 - 501
4111D1 - 501

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Components

#1: Protein
Catalase


Mass: 60001.129 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) 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.: 121 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 273 K
Method: sitting drop vapor diffusion using polymer-induced heteronucleation
pH: 6.8
Details: 0.05 M sodium phosphate pH 6.8, 12% PEG 4000, sitting drop vapor diffusion using polymer-induced heteronucleation, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2009 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 60233 / Num. obs: 60233 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.73
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.95 / Num. unique all: 2672 / % possible all: 86.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4blc
Resolution: 2.69→39.98 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 27.221 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 3041 5.1 %RANDOM
Rwork0.20347 ---
all0.20548 57155 --
obs0.20539 57155 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16068 0 364 121 16553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02216964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.98523132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24551992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60923.665884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.893152596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.75915124
X-RAY DIFFRACTIONr_chiral_restr0.1040.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113508
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4231.59992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.855216160
X-RAY DIFFRACTIONr_scbond_it1.3736972
X-RAY DIFFRACTIONr_scangle_it2.3424.56972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4018 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.190.05
Btight positional0.180.05
Ctight positional0.180.05
Dtight positional0.20.05
Atight thermal0.320.5
Btight thermal0.240.5
Ctight thermal0.250.5
Dtight thermal0.240.5
LS refinement shellResolution: 2.692→2.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 226 -
Rwork0.3 3573 -
obs-3573 83.55 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.34022.21480.34995.72494.09946.8935-0.2306-0.0467-0.07520.6001-0.08060.60170.5439-0.36340.31110.2504-0.02490.09820.33710.00550.200652.51152.847157.286
20.17260.0010.0190.73030.21760.2869-0.01330.00780.04230.04010.0244-0.07320.0328-0.0416-0.01110.1441-0.0152-0.00250.27450.01560.124959.10180.355149.142
34.18842.80640.1632.4870.91571.55270.3185-0.5837-0.6180.2547-0.031-0.5819-0.0544-0.0072-0.28760.2069-0.0222-0.12320.33590.04480.184963.44176.745166.765
40.49390.07480.08240.63970.02020.4137-0.028-0.05030.092-0.03050.05510.06030.0081-0.0009-0.02710.13980.0151-0.00420.2564-0.00580.131650.59886.052147.61
51.88440.16320.08451.35461.92372.1843-0.06420.06440.0399-0.1312-0.0980.1465-0.1484-0.18210.16220.21640.0026-0.0250.29010.09440.159241.76288.546127.427
60.73070.1620.31150.85240.27092.0326-0.0551-0.16810.0990.16780.0664-0.1318-0.2091-0.0113-0.01130.1799-0.0105-0.05410.2454-0.02140.184771.398101.223162.378
712.76690.98953.8571-0.91595.74915.6927-0.1493-0.89082.12430.68080.3769-0.36191.13170.2792-0.22760.62170.1623-0.86060.1173-0.25151.380783.39395.915170.225
80.0245-0.2116-0.16280.4680.51741.24190.0246-0.00890.0395-0.14780.0872-0.2148-0.11920.1812-0.11180.2474-0.03290.18090.3026-0.03210.363283.69359.903109.441
90.3057-0.00330.09560.4427-0.12580.1255-0.07680.03480.0419-0.21350.0291-0.11250.00510.00270.04770.278-0.03930.04040.2643-0.0110.132465.19592.033112.249
101.31790.22290.6971.0172-0.11691.2472-0.14560.03940.1413-0.36750.03720.0561-0.1305-0.13530.10840.2809-0.0522-0.05730.25740.02230.078844.43397.74105.516
116.5793-5.31580.25193.6977-0.62130.63780.1694-0.1965-0.7915-0.316-0.09820.66140.4036-0.0942-0.07110.2444-0.1218-0.0590.6571-0.04110.306231.84275.012115.099
120.2935-0.0118-0.02381.03680.4160.2527-0.0213-0.04230.0188-0.11740.04150.08460.0234-0.0901-0.02020.2139-0.0544-0.03170.3178-0.00750.116848.83168.475122.716
130.43360.18910.10840.77040.10150.39610.00580.02120.0558-0.25490.0471-0.04110.0893-0.0452-0.05290.3204-0.0350.03130.239-0.01040.107659.93754.778105.779
140.03970.03620.06950.3676-0.23840.2608-0.0268-0.0283-0.0094-0.16440.0585-0.01340.1099-0.0789-0.03170.2782-0.05720.00280.2653-0.02310.135455.70950.306118.285
15-0.3271-0.3741-0.002715.1242.24930.1306-0.02290.0431-0.0558-0.33970.01190.85010.00390.04740.0110.1419-0.0129-0.04190.3080.0030.281857.23954.185147.094
160.73810.4185-0.120.9389-0.82561.9528-0.02030.1561-0.1363-0.2040.0288-0.2260.11130.0143-0.00850.39050.05360.0920.2236-0.05410.120170.03847.91397.817
177.0463-2.6534.700611.3925-5.59313.2277-0.76960.70270.60890.29110.0356-1.0662-0.37120.27660.73410.1173-0.1014-0.01260.2899-0.07290.664691.22592.878145.915
180.0716-0.0326-0.0031.0637-0.05010.2734-0.0609-0.01020.0027-0.02680.0779-0.21590.03250.0264-0.01710.1282-0.00880.00180.2544-0.01530.246781.14465.329142.675
190.80410.4561-0.07081.266-0.04130.4418-0.0262-0.0972-0.0940.05590.0332-0.34540.060.1026-0.00710.10540.0233-0.00990.264-0.00690.304692.37158.237149.135
200.93090.68790.42080.70070.39460.2535-0.0467-0.0069-0.1055-0.16030.0391-0.1931-0.03150.06330.00760.2126-0.00660.07550.2479-0.02520.241881.96264.258130.462
211.6155-1.59220.3582.0488-1.8712.22250.0081-0.11440.402-0.25890.1197-0.33770.32460.0014-0.12780.2227-0.04660.07110.2251-0.13180.488783.93857.406114.963
220.9749-0.2664-0.21940.7387-0.77871.92940.0489-0.20110.01010.18030.0258-0.1660.2682-0.0225-0.07460.3378-0.0347-0.1350.22620.03360.262277.00845.115162.643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 24
2X-RAY DIFFRACTION2A25 - 235
3X-RAY DIFFRACTION3A236 - 262
4X-RAY DIFFRACTION4A263 - 390
5X-RAY DIFFRACTION5A391 - 427
6X-RAY DIFFRACTION6A428 - 490
7X-RAY DIFFRACTION7A491 - 501
8X-RAY DIFFRACTION8B3 - 53
9X-RAY DIFFRACTION9B54 - 411
10X-RAY DIFFRACTION10B412 - 501
11X-RAY DIFFRACTION11C3 - 24
12X-RAY DIFFRACTION12C25 - 113
13X-RAY DIFFRACTION13C114 - 262
14X-RAY DIFFRACTION14C263 - 391
15X-RAY DIFFRACTION15C392 - 411
16X-RAY DIFFRACTION16C412 - 501
17X-RAY DIFFRACTION17D3 - 24
18X-RAY DIFFRACTION18D25 - 233
19X-RAY DIFFRACTION19D234 - 320
20X-RAY DIFFRACTION20D321 - 389
21X-RAY DIFFRACTION21D390 - 427
22X-RAY DIFFRACTION22D428 - 501

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