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- PDB-7bxd: Crystal structure of Ca_00815 -

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Basic information

Entry
Database: PDB / ID: 7bxd
TitleCrystal structure of Ca_00815
ComponentsGDSL-like protein
KeywordsHYDROLASE / acyl-hydrolase
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / GDSL-like protein
Function and homology information
Biological speciesCollinsella aerofaciens ATCC 25986 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsFan, C.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: To Be Published
Title: Crystal structure of Ca_00815
Authors: Fan, C.P.
History
DepositionApr 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDSL-like protein


Theoretical massNumber of molelcules
Total (without water)26,4801
Polymers26,4801
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9200 Å2
2
A: GDSL-like protein

A: GDSL-like protein

A: GDSL-like protein


Theoretical massNumber of molelcules
Total (without water)79,4393
Polymers79,4393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5480 Å2
ΔGint-12 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.420, 113.420, 113.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-574-

HOH

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Components

#1: Protein GDSL-like protein / Ca_00815


Mass: 26479.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collinsella aerofaciens ATCC 25986 (bacteria)
Gene: COLAER_00815 / Production host: Escherichia coli (E. coli) / References: UniProt: A4E8S4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M KCL, 0.1M pH 6.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.18→46.3 Å / Num. obs: 79909 / % possible obs: 99.9 % / Redundancy: 38.9 % / Biso Wilson estimate: 15.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.012 / Rrim(I) all: 0.076 / Rsym value: 0.075 / Net I/av σ(I): 26.9 / Net I/σ(I): 26.9
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 32.2 % / Rmerge(I) obs: 2.931 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3925 / CC1/2: 0.593 / Rpim(I) all: 0.516 / Rrim(I) all: 2.975 / Rsym value: 2.931 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DCI

3dci


Resolution: 1.18→35.87 Å / SU ML: 0.1132 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.0389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1545 1974 2.47 %
Rwork0.1409 77925 -
obs0.1412 79899 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.31 Å2
Refinement stepCycle: LAST / Resolution: 1.18→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 277 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031700
X-RAY DIFFRACTIONf_angle_d1.07742312
X-RAY DIFFRACTIONf_chiral_restr0.0869255
X-RAY DIFFRACTIONf_plane_restr0.0087306
X-RAY DIFFRACTIONf_dihedral_angle_d3.4413958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.27961360.24725511X-RAY DIFFRACTION99.1
1.21-1.240.23571400.20025485X-RAY DIFFRACTION100
1.24-1.280.19341370.17715572X-RAY DIFFRACTION100
1.28-1.320.19011430.15795514X-RAY DIFFRACTION99.98
1.32-1.360.18741450.1485559X-RAY DIFFRACTION100
1.36-1.420.16081410.13425501X-RAY DIFFRACTION100
1.42-1.480.14531390.12055584X-RAY DIFFRACTION100
1.48-1.560.14091420.11375530X-RAY DIFFRACTION99.98
1.56-1.660.12361390.11265542X-RAY DIFFRACTION99.98
1.66-1.790.15051400.12315585X-RAY DIFFRACTION99.98
1.79-1.970.13741470.12755584X-RAY DIFFRACTION100
1.97-2.250.14341400.13245557X-RAY DIFFRACTION100
2.25-2.840.15931420.14735641X-RAY DIFFRACTION100
2.84-35.870.15411430.14785760X-RAY DIFFRACTION99.98

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