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- PDB-3fgt: Two chain form of the 66.3 kDa protein from mouse lacking the lin... -

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Basic information

Entry
Database: PDB / ID: 3fgt
TitleTwo chain form of the 66.3 kDa protein from mouse lacking the linker peptide
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 / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / lysosomal lumen / lysosome
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
Chem-7PE / ACETATE ION / Putative phospholipase B-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 / Item: _software.name
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 / diffrn_source / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _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)65,47817
Polymers63,2512
Non-polymers2,22615
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-30 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.570, 88.220, 63.270
Angle α, β, γ (deg.)90.00, 98.10, 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, 3 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.: 1
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 6 types, 311 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.4→29.488 Å / Num. all: 31093 / Num. obs: 31031 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.5 / Num. measured all: 15401 / Num. unique all: 4544 / Rsym value: 0.459 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBX

3fbx


Resolution: 2.4→29.488 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU B: 5.671 / SU ML: 0.135 / SU R Cruickshank DPI: 0.266 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20745 1557 5 %RANDOM
Rwork0.16581 ---
obs0.168 29465 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.37 Å2 / Biso mean: 28.054 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.07 Å2
2---0.49 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 146 299 4634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9836082
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01724.019209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19915691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22648
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23053
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6341.52638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22424249
X-RAY DIFFRACTIONr_scbond_it1.87631945
X-RAY DIFFRACTIONr_scangle_it2.9154.51829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 102 -
Rwork0.198 2172 -
all-2274 -
obs--99.78 %

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