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- PDB-3fgw: One chain form of the 66.3 kDa protein -

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Basic information

Entry
Database: PDB / ID: 3fgw
TitleOne chain form of the 66.3 kDa protein
ComponentsPutative phospholipase B-like 2
KeywordsHYDROLASE / alpha beta / glycosylated / disulphide bonds / N-terminal hydrolase fold / occupied pocket / one 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
Penicillin V Acylase; Chain A - #30 / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Putative phospholipase B-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 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.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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,62316
Polymers63,1851
Non-polymers2,43815
Water2,882160
1
A: Putative phospholipase B-like 2
hetero molecules

A: Putative phospholipase B-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,24632
Polymers126,3712
Non-polymers4,87630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8220 Å2
ΔGint-8 kcal/mol
Surface area39580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.690, 88.110, 73.550
Angle α, β, γ (deg.)90.00, 111.10, 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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Protein , 1 types, 1 molecules A

#1: Protein Putative phospholipase B-like 2 / 66.3 kDa protein / Lamina ancestor homolog 2 / LAMA-like protein 2 / 76 kDa protein / p76 / ...66.3 kDa protein / Lamina ancestor homolog 2 / LAMA-like protein 2 / 76 kDa protein / p76 / Putative phospholipase B-like 2 28 kDa form / Putative phospholipase B-like 2 40 kDa form / Putative phospholipase B-like 2 15 kDa form


Mass: 63185.285 Da / Num. of mol.: 1
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, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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 , 4 types, 171 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12% (w/v) PEG 4000, 100mM 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: 14.1 / Wavelength: 1.8 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.8→46.07 Å / Num. obs: 21117 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 3 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Rsym value: 0.43 / % possible all: 96.2

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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
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBX

3fbx


Resolution: 2.8→46.07 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.855 / SU B: 11.5 / SU ML: 0.227 / SU R Cruickshank DPI: 0.539 / SU Rfree: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.539 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; CNS 1.21 was also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.24921 1072 5.1 %RANDOM
Rwork0.2229 19835 --
obs0.22423 20907 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 32.212 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20.08 Å2
2---5.06 Å20 Å2
3---6.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 107 160 4487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224446
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.9716059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74524.155207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43715684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023396
X-RAY DIFFRACTIONr_nbd_refined0.1870.22215
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.27
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 69 -
Rwork0.364 1431 -
all-1500 -
obs--95.54 %

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