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- PDB-4tx1: The crystal structure of carbohydrate acetylesterase family membe... -

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Basic information

Entry
Database: PDB / ID: 4tx1
TitleThe crystal structure of carbohydrate acetylesterase family member from Sinorhizobium meliloti
ComponentsEsterase
KeywordsHYDROLASE / SGNH-hydrolase / acetylesterase / SGNH-family
Function / homology
Function and homology information


arylesterase / arylesterase activity
Similarity search - Function
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
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKim, K. / Kim, S.S. / Pandian, R. / Ngo, T.D.
CitationJournal: Febs Lett. / Year: 2015
Title: Structural and biochemical characterization of a carbohydrate acetylesterase from Sinorhizobium meliloti 1021.
Authors: Kim, K. / Ryu, B.H. / Kim, S.S. / An, D.R. / Ngo, T.D. / Pandian, R. / Kim, K.K. / Kim, T.D.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase


Theoretical massNumber of molelcules
Total (without water)73,0553
Polymers73,0553
Non-polymers00
Water12,629701
1
A: Esterase
B: Esterase
C: Esterase

A: Esterase
B: Esterase
C: Esterase


Theoretical massNumber of molelcules
Total (without water)146,1096
Polymers146,1096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area13810 Å2
ΔGint-63 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.238, 126.238, 191.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

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Components

#1: Protein Esterase


Mass: 24351.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Gene: R01448, SMc01033 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7APD5, arylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.76 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 285 K / Method: microbatch
Details: Crystal Screen I No. 44 0.2 M magnesium formate dehydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 77446 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.503 / Net I/av σ(I): 59.545 / Net I/σ(I): 15.5 / Num. measured all: 1076704
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.789.40.46837611.31198.5
1.78-1.8111.20.42938521.331100
1.81-1.85130.3638291.344100
1.85-1.8913.40.31138081.375100
1.89-1.9313.70.25938551.427100
1.93-1.9713.90.22338271.444100
1.97-2.0214.10.18738261.468100
2.02-2.0714.30.15538831.493100
2.07-2.1414.50.13838091.509100
2.14-2.214.60.11238641.537100
2.2-2.2814.70.09638621.566100
2.28-2.3814.80.08838491.546100
2.38-2.4814.80.07438811.55100
2.48-2.6114.80.06538691.556100
2.61-2.7814.80.05738741.531100
2.78-2.9914.80.04839111.518100
2.99-3.2914.70.0438951.525100
3.29-3.7714.50.03539271.52299.9
3.77-4.7514.30.03339591.54399.7
4.75-5013.60.03441051.79498.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q0Q

2q0q


Resolution: 1.75→32.61 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.763 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 3888 5 %RANDOM
Rwork0.1546 73375 --
obs0.1564 77263 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.76 Å2 / Biso mean: 18.62 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.75→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 0 701 5522
Biso mean---32.63 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194907
X-RAY DIFFRACTIONr_bond_other_d0.0040.023246
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9646678
X-RAY DIFFRACTIONr_angle_other_deg1.237898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56723.318211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3315761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1141539
X-RAY DIFFRACTIONr_chiral_restr0.1650.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 280 -
Rwork0.203 5059 -
all-5339 -
obs--99.26 %

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