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- PDB-3fgr: Two chain form of the 66.3 kDa protein at 1.8 Angstroem -

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Basic information

Entry
Database: PDB / ID: 3fgr
TitleTwo chain form of the 66.3 kDa protein at 1.8 Angstroem
Components(Putative phospholipase B-like 2 ...) x 2
KeywordsHYDROLASE / alpha beta / glycosylated / disulphide bonds / N-terminal nucleophile hydrolase fold / two chain form / Glycoprotein / Lipid degradation / Lysosome
Function / homology
Function and homology information


phospholipase activity / phospholipid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lysosomal lumen / lysosome / extracellular region
Similarity search - Function
Phospholipase B-like, domain 2 / Phospholipase B-like, domain 1 / Penicillin V Acylase; Chain A - #20 / Phospholipase B-like / Phospholipase B-like, domain 1 / Phospholipase B-like, domain 2 / Phospholipase B-like, domain 3 / Phospholipase B / Penicillin V Acylase; Chain A / Penicillin Amidohydrolase; domain 1 ...Phospholipase B-like, domain 2 / Phospholipase B-like, domain 1 / Penicillin V Acylase; Chain A - #20 / Phospholipase B-like / Phospholipase B-like, domain 1 / Phospholipase B-like, domain 2 / Phospholipase B-like, domain 3 / Phospholipase B / Penicillin V Acylase; Chain A / Penicillin Amidohydrolase; domain 1 / Complement Module; domain 1 / Ribbon / 4-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / XENON / Putative phospholipase B-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLakomek, K. / Dickmanns, A. / Ficner, R.
Citation
Journal: Bmc Struct.Biol. / Year: 2009
Title: Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography
Authors: Lakomek, K. / Dickmanns, A. / Kettwig, M. / Urlaub, H. / Ficner, R. / Luebke, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse
Authors: Lakomek, K. / Dickmanns, A. / Mueller, U. / Kollmann, K. / Deuschl, F. / Berndt, A. / Luebke, T. / Ficner, R.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phospholipase B-like 2 28 kDa form
B: Putative phospholipase B-like 2 40 kDa form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,04922
Polymers63,2512
Non-polymers2,79820
Water10,377576
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-34 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.737, 89.560, 64.811
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number5
Space group name H-MC121
Detailsauthor states that the biological unit is unknown

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Components

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Putative phospholipase B-like 2 ... , 2 types, 2 molecules AB

#1: Protein Putative phospholipase B-like 2 28 kDa form / Lamina ancestor homolog 2 / LAMA-like protein 2 / 76 kDa protein / p76 / 66.3 kDa protein


Mass: 22774.531 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 47-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/RV / Gene: AAG44101 / Plasmid: PCDNA3.1/HYGRO(+) / Cell (production host): fibrosarcoma cell / Cell line (production host): HT1080 / Production host: Homo sapiens (human)
References: UniProt: Q3TCN2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Protein Putative phospholipase B-like 2 40 kDa form / Lamina ancestor homolog 2 / LAMA-like protein 2 / 76 kDa protein / p76 / 66.3 kDa protein


Mass: 40476.836 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 249-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/RV / Gene: AAG44101 / Plasmid: PCDNA3.1/HYGRO(+) / Cell (production host): fibrosarcoma cell / Cell line (production host): HT1080 / Production host: Homo sapiens (human)
References: UniProt: Q3TCN2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 2 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 591 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12% (w/v) PEG 4000, 200mM NH4AC, 100mM NaAc/HAc pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 91683 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 32.075
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.419 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBX

3fbx


Resolution: 1.8→29.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.899 / SU B: 1.607 / SU ML: 0.052 / SU R Cruickshank DPI: 0.085 / SU Rfree: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18163 3839 4.9 %RANDOM
Rwork0.15163 73846 --
obs0.15314 77685 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 24.259 Å2 / Biso min: 9.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0.44 Å2
2---0.51 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 174 576 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9846282
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65423.944213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9621527
X-RAY DIFFRACTIONr_chiral_restr0.1210.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023506
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.32360
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.53157
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5853
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9551.52688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77724353
X-RAY DIFFRACTIONr_scbond_it2.92632019
X-RAY DIFFRACTIONr_scangle_it4.5344.51906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 259 -
Rwork0.203 5489 -
all-5748 -
obs--99.79 %

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