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- PDB-8gr2: Crystal structure of the GDSL-family esterase CJ0610C from Campyl... -

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Basic information

Entry
Database: PDB / ID: 8gr2
TitleCrystal structure of the GDSL-family esterase CJ0610C from Campylobacter jejuni
ComponentsDUF459 domain-containing protein
KeywordsHYDROLASE / GDSL-family esterase
Function / homologySGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / DUF459 domain-containing protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKi, D.U. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural and biochemical analysis of the GDSL-family esterase CJ0610C from Campylobacter jejuni.
Authors: Ki, D.U. / Song, W.S. / Yoon, S.I.
History
DepositionAug 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF459 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4013
Polymers26,2091
Non-polymers1922
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.208, 55.208, 136.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein DUF459 domain-containing protein / CJ0610C


Mass: 26208.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BBR99_07950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A400R5A3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, Bis-Tris, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 28325 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.996 / Net I/σ(I): 32.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1438 / CC1/2: 0.734 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 model

Resolution: 1.65→27.8 Å / SU ML: 0.1961 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 1440 5.1 %
Rwork0.1666 26813 -
obs0.1677 28253 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 10 124 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561707
X-RAY DIFFRACTIONf_angle_d0.76912314
X-RAY DIFFRACTIONf_chiral_restr0.0539261
X-RAY DIFFRACTIONf_plane_restr0.0048291
X-RAY DIFFRACTIONf_dihedral_angle_d14.51481008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.32691460.24722694X-RAY DIFFRACTION100
1.71-1.780.28231500.21482673X-RAY DIFFRACTION99.93
1.78-1.860.24891300.20072663X-RAY DIFFRACTION100
1.86-1.960.22231470.18222686X-RAY DIFFRACTION99.96
1.96-2.080.17991540.1612662X-RAY DIFFRACTION100
2.08-2.240.15821290.15462703X-RAY DIFFRACTION100
2.24-2.460.17051380.15352687X-RAY DIFFRACTION100
2.46-2.820.21631610.17072673X-RAY DIFFRACTION99.96
2.82-3.550.16641410.16532684X-RAY DIFFRACTION99.82
3.55-27.80.1691440.15452688X-RAY DIFFRACTION98.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.692045296060.03172573795590.5831048634660.2670711995210.3570004714263.674306195310.1074787073640.106951633331-0.273949433746-0.0242477504541-0.03839024258180.06564030225970.4100474946540.174582736012-0.03592323348610.2522603759510.0233466074239-0.02475055288050.136499562408-0.01922858092890.208245585954-2.48471964494-30.99808818780.128223549394
21.91786948269-0.4221531343280.4248187826621.8487148376-0.1395116064021.659854623350.125586753372-0.00686066871519-0.224111462677-0.0416270456058-0.06487262798290.1135057718890.216219557523-0.2298336119-0.03043685569560.159726239566-0.0374033485805-0.01605273357650.156587520991-0.004191418806450.131479574256-15.2076873626-23.3246412554-1.85530702045
33.389103719350.116735191923-1.254869034518.27240593138-6.087550996328.157215010940.0698118315846-0.1820129366570.2076001610730.244155481617-0.0837082414159-0.0131474951338-0.408404159539-0.04766871732980.01067051721390.1639129846850.00708859986551-0.02117489399680.191991519667-0.03128695944040.143765455194-9.48037900788-15.11401243446.10927218878
44.21264733510.792713622099-0.3477253407083.08031186511-0.8923327299053.969660684180.02469259069030.1800979188020.147757205717-0.08260898029270.0290714633273-0.1621165022230.03464084724840.502614931224-0.02763936032220.1371609795590.00688598921785-0.0124702571640.178166083256-0.02186534361350.1552313819384.85318815266-21.13355750741.05783332323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 271 )
4X-RAY DIFFRACTION4chain 'A' and (resid 272 through 328 )

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