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- PDB-6gs0: Native Glucuronoyl Esterase from Opitutus terrae -

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Basic information

Entry
Database: PDB / ID: 6gs0
TitleNative Glucuronoyl Esterase from Opitutus terrae
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Carbohydrate Esterase
Function / homologyAlpha/Beta hydrolase fold / metal ion binding / TRIETHYLENE GLYCOL / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLo Leggio, L. / Larsbrink, J. / Meland Knudsen, R. / Mazurkewich, S. / Navarro Poulsen, J.C.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk Foundation NNF17OC0027698 Denmark
European UnionInterreg-programmet for Oresund-Kattegat-Skagerrak Denmark
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion.
Authors: Arnling Baath, J. / Mazurkewich, S. / Knudsen, R.M. / Poulsen, J.N. / Olsson, L. / Lo Leggio, L. / Larsbrink, J.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81713
Polymers43,9881
Non-polymers82912
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint8 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.361, 44.263, 50.027
Angle α, β, γ (deg.)75.863, 66.326, 70.876
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative acetyl xylan esterase


Mass: 43988.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4

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Non-polymers , 5 types, 378 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir composition: 0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulfate and 0.3 M Sodium nitrate, 0.05 M Tris and 0,05 M BICINE, 12.5 % v/v MPD, 12.5 % w/v PEG1000 and 12.5 % ...Details: Reservoir composition: 0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulfate and 0.3 M Sodium nitrate, 0.05 M Tris and 0,05 M BICINE, 12.5 % v/v MPD, 12.5 % w/v PEG1000 and 12.5 % w/v PEG3350 Drop size and composition: sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 3:1 using 45 mg/ml of OtCE15A in 20 mM TRIS pH 8.0
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.34→45.43 Å / Num. obs: 63925 / % possible obs: 88.9 % / Redundancy: 2.95 % / Biso Wilson estimate: 14.79 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.101 / Net I/σ(I): 6.35
Reflection shellResolution: 1.34→1.37 Å / Redundancy: 2.93 % / Rmerge(I) obs: 1.073 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 13846 / CC1/2: 0.534 / Rrim(I) all: 1.159 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot0.8.9 ELmodel building
XDSBUILD = 20180126data reduction
PHENIX1.13_2998phasing
XDSBUILD = 20180126data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GRW

6grw


Resolution: 1.34→45.43 Å / SU ML: 0.1991 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.9743
RfactorNum. reflection% reflection
Rfree0.2073 2645 4.14 %
Rwork0.173 --
obs0.1745 63886 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 1.34→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 52 366 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813346
X-RAY DIFFRACTIONf_angle_d1.07394565
X-RAY DIFFRACTIONf_chiral_restr0.0749478
X-RAY DIFFRACTIONf_plane_restr0.0086608
X-RAY DIFFRACTIONf_dihedral_angle_d18.30921219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.37981400.41443208X-RAY DIFFRACTION88.78
1.36-1.390.44461380.38613243X-RAY DIFFRACTION88.55
1.39-1.420.36731300.36523024X-RAY DIFFRACTION83.86
1.42-1.450.38161400.34053217X-RAY DIFFRACTION89.16
1.45-1.480.32411420.3033287X-RAY DIFFRACTION90.81
1.48-1.520.31161390.27623275X-RAY DIFFRACTION90.25
1.52-1.560.28811330.26123258X-RAY DIFFRACTION90.33
1.56-1.610.27351460.24463226X-RAY DIFFRACTION89.04
1.61-1.660.23231330.21893144X-RAY DIFFRACTION86.26
1.66-1.720.25131460.19293040X-RAY DIFFRACTION85.19
1.72-1.790.21131440.17613281X-RAY DIFFRACTION91.04
1.79-1.870.17361370.15933331X-RAY DIFFRACTION91.48
1.87-1.970.19151310.15123261X-RAY DIFFRACTION90
1.97-2.090.16861480.1523184X-RAY DIFFRACTION88.17
2.09-2.250.21231370.14993135X-RAY DIFFRACTION86.91
2.25-2.480.18781390.14273365X-RAY DIFFRACTION92.77
2.48-2.840.18841440.14463280X-RAY DIFFRACTION90.8
2.84-3.580.16991390.13633162X-RAY DIFFRACTION87.33
3.58-45.450.16841390.13923320X-RAY DIFFRACTION91.56

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