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- PDB-5hoe: Crystal structrue of Est24, a carbohydrate acetylesterase from Si... -

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Basic information

Entry
Database: PDB / ID: 5hoe
TitleCrystal structrue of Est24, a carbohydrate acetylesterase from Sinorhizobium meliloti
ComponentsHydrolase
KeywordsHYDROLASE / Est24 / carbohydrate acetylesterase / Sinorhizobium meliloti
Function / homology
Function and homology information


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
PHOSPHATE ION / Hydrolase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsOh, C. / Ryu, B.H. / An, D.R. / Nguyen, D.D. / Yoo, W. / Kim, T. / Ngo, D.T. / Kim, H.S. / Park, J.S. / Kim, K.K. / Kim, T.D.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Korea Government2012R1A1A2000910 Korea, Republic Of
Rural Development AdministrationSSAC PJ008107 Korea, Republic Of
National Research Foundation of Korea2011-0028878 Korea, Republic Of
CitationJournal: Febs Lett. / Year: 2016
Title: Structural and Biochemical Characterization of an Octameric Carbohydrate Acetylesterase from Sinorhizobium meliloti.
Authors: Oh, C. / Ryu, B.H. / An, D.R. / Nguyen, D.D. / Yoo, W. / Kim, T. / Ngo, T.D. / Kim, H.S. / Kim, K.K. / Kim, T.D.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,93910
Polymers99,9944
Non-polymers9456
Water16,141896
1
A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,87820
Polymers199,9898
Non-polymers1,88912
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23550 Å2
ΔGint-220 kcal/mol
Surface area57920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.089, 88.626, 86.148
Angle α, β, γ (deg.)90.00, 114.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hydrolase /


Mass: 24998.572 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMa1993 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q92XZ6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: 0.2 M ammonium phosphate, (pH 4.6) 20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→35.864 Å / Num. obs: 145939 / % possible obs: 93.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.3
Reflection shellResolution: 1.451→1.503 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q0Q

2q0q


Resolution: 1.45→35.86 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.216 7346 5.03 %
Rwork0.172 --
obs0.174 145930 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 58 896 7486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116936
X-RAY DIFFRACTIONf_angle_d1.3479459
X-RAY DIFFRACTIONf_dihedral_angle_d13.3882519
X-RAY DIFFRACTIONf_chiral_restr0.0771022
X-RAY DIFFRACTIONf_plane_restr0.0071225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.46750.31151370.25273095X-RAY DIFFRACTION63
1.4675-1.48480.3031950.22123724X-RAY DIFFRACTION75
1.4848-1.50290.27452140.2094023X-RAY DIFFRACTION81
1.5029-1.52190.24531930.19644216X-RAY DIFFRACTION86
1.5219-1.54190.2552380.18534506X-RAY DIFFRACTION92
1.5419-1.56310.252750.17084775X-RAY DIFFRACTION97
1.5631-1.58540.23392600.16924917X-RAY DIFFRACTION100
1.5854-1.60910.22592760.17134895X-RAY DIFFRACTION100
1.6091-1.63420.25982570.16334944X-RAY DIFFRACTION100
1.6342-1.6610.22412620.16334904X-RAY DIFFRACTION100
1.661-1.68960.24922840.16544891X-RAY DIFFRACTION100
1.6896-1.72040.19712250.15414945X-RAY DIFFRACTION100
1.7204-1.75350.21952610.15834888X-RAY DIFFRACTION100
1.7535-1.78920.22682450.16524960X-RAY DIFFRACTION100
1.7892-1.82810.21712530.15594914X-RAY DIFFRACTION100
1.8281-1.87070.20932800.15864906X-RAY DIFFRACTION100
1.8707-1.91750.20442460.15544898X-RAY DIFFRACTION100
1.9175-1.96930.20072830.15654934X-RAY DIFFRACTION100
1.9693-2.02720.18822800.15524873X-RAY DIFFRACTION100
2.0272-2.09270.21883010.15624886X-RAY DIFFRACTION100
2.0927-2.16740.21582520.16324918X-RAY DIFFRACTION99
2.1674-2.25420.17722650.15414855X-RAY DIFFRACTION99
2.2542-2.35680.19962400.15484862X-RAY DIFFRACTION98
2.3568-2.4810.20152590.15854841X-RAY DIFFRACTION98
2.481-2.63640.18762330.15874790X-RAY DIFFRACTION97
2.6364-2.83990.20712770.16964701X-RAY DIFFRACTION96
2.8399-3.12550.19652290.17274577X-RAY DIFFRACTION92
3.1255-3.57750.24252230.19574322X-RAY DIFFRACTION87
3.5775-4.50580.22692050.18793735X-RAY DIFFRACTION75
4.5058-35.87520.24861980.21253889X-RAY DIFFRACTION77

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