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- PDB-4bwc: X-ray structure of a phospholiapse B like protein 1 from bovine k... -

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Basic information

Entry
Database: PDB / ID: 4bwc
TitleX-ray structure of a phospholiapse B like protein 1 from bovine kidneys
Components(PHOSPHOLIPASE B-LIKE ...) x 2
KeywordsHYDROLASE / GLYCOSYLATION / LYSOSOMAL STORAGE DISORDERS
Function / homology
Function and homology information


Hydrolysis of LPC / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / phospholipase activity / phospholipid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / 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
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Phospholipase B-like 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRepo, H. / Kuokkanen, E. / Oksanen, E. / Goldman, A. / Heikinheimo, P.
CitationJournal: Proteins / Year: 2014
Title: Is the Bovine Lysosomal Phospholipase B-Like Protein an Amidase?
Authors: Repo, H. / Kuokkanen, E. / Oksanen, E. / Goldman, A. / Heikinheimo, P.
History
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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: PHOSPHOLIPASE B-LIKE 1
B: PHOSPHOLIPASE B-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,87810
Polymers56,6822
Non-polymers2,1968
Water3,315184
1
A: PHOSPHOLIPASE B-LIKE 1
B: PHOSPHOLIPASE B-LIKE 1
hetero molecules

A: PHOSPHOLIPASE B-LIKE 1
B: PHOSPHOLIPASE B-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,75620
Polymers113,3654
Non-polymers4,39116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area20580 Å2
ΔGint-78.2 kcal/mol
Surface area37250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.370, 97.370, 140.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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PHOSPHOLIPASE B-LIKE ... , 2 types, 2 molecules AB

#1: Protein PHOSPHOLIPASE B-LIKE 1 / LAMA-LIKE PROTEIN 1 / LAMINA ANCESTOR HOMOLOG 1 / PHOSPHOLIPASE B DOMAIN-CONTAINING PROTEIN 1 / ...LAMA-LIKE PROTEIN 1 / LAMINA ANCESTOR HOMOLOG 1 / PHOSPHOLIPASE B DOMAIN-CONTAINING PROTEIN 1 / PHOSPHOLIPASE B-LIKE PROTEIN 1


Mass: 19522.355 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SEGMENT, RESIDUES 36-205 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: KIDNEY
References: UniProt: Q9GL30, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Protein PHOSPHOLIPASE B-LIKE 1 / LAMA-LIKE PROTEIN 1 / LAMINA ANCESTOR HOMOLOG 1 / PHOSPHOLIPASE B DOMAIN-CONTAINING PROTEIN 1 / ...LAMA-LIKE PROTEIN 1 / LAMINA ANCESTOR HOMOLOG 1 / PHOSPHOLIPASE B DOMAIN-CONTAINING PROTEIN 1 / PHOSPHOLIPASE B-LIKE PROTEIN 1


Mass: 37160.078 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SEGMENT, RESIDUES 225-545 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: KIDNEY
References: UniProt: Q9GL30, 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.: 3
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
#5: 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 , 4 types, 187 molecules

#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M TRIS-CL PH 7, 40% PEG 300, 5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.89→46.98 Å / Num. obs: 62608 / % possible obs: 99.8 % / Observed criterion σ(I): 2.91 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.74
Reflection shellResolution: 1.89→2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.91 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBX

3fbx


Resolution: 1.89→46.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.871 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23061 3127 5 %RANDOM
Rwork0.1881 ---
obs0.19019 59478 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.379 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 143 184 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.024272
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.9835795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7515493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35823.969194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74415693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6471517
X-RAY DIFFRACTIONr_chiral_restr0.1550.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213215
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.887→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 204 -
Rwork0.294 4095 -
obs--99.03 %

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