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- PDB-4hyq: Crystal structure of phospholipase A1 from Streptomyces albidofla... -

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Basic information

Entry
Database: PDB / ID: 4hyq
TitleCrystal structure of phospholipase A1 from Streptomyces albidoflavus NA297
Componentsphospholipase A1
KeywordsHYDROLASE / lipase / glycerophospholipid
Function / homology
Function and homology information


triglyceride catabolic process / triacylglycerol lipase / triacylglycerol lipase activity
Similarity search - Function
Streptomyces scabies esterase-like / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
triacylglycerol lipase
Similarity search - Component
Biological speciesStreptomyces albidoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMurayama, K. / Sugimori, D.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297
Authors: Murayama, K. / Kano, K. / Matsumoto, Y. / Sugimori, D.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phospholipase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4382
Polymers24,2001
Non-polymers2381
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.550, 67.550, 96.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein phospholipase A1


Mass: 24199.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albidoflavus (bacteria) / Strain: NA297 / Plasmid: pUC702/pla / Production host: Streptomyces lividans (bacteria) / References: UniProt: K0J3J2*PLUS, phospholipase A1
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE UNP SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS ...THE UNP SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS BEEN DEPOSITED TO GENBANK, BAM45317

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M ammonium sulfate, 3% PEGMME2000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.1 Å / Num. obs: 26008 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.105 / Net I/σ(I): 29.5
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 5.8 / Rsym value: 0.618 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ESC

1esc


Resolution: 1.75→37.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1591373 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1256 4.8 %RANDOM
Rwork0.186 ---
obs0.186 25973 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3638 Å2 / ksol: 0.386993 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å21.13 Å20 Å2
2--1.84 Å20 Å2
3----3.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.75→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 16 218 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 197 4.8 %
Rwork0.21 3904 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param1PE.top
X-RAY DIFFRACTION31PE.param

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