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- PDB-6grw: Glucuronoyl Esterase from Opitutus terrae (Au derivative) -

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Basic information

Entry
Database: PDB / ID: 6grw
TitleGlucuronoyl Esterase from Opitutus terrae (Au derivative)
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Carbohydrate Esterase
Function / homologyAlpha/Beta hydrolase fold / : / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)44,89912
Polymers43,9881
Non-polymers91111
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-24 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.693, 44.608, 50.558
Angle α, β, γ (deg.)76.573, 67.172, 70.648
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 , 6 types, 413 molecules

#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir composition for crystal growth: 0.03M Magnesium chloride, 0.03 M calcium chloride, 0.05M imidazole, 0.05M MES, 10% v/v MPD, 10% w/v PEG 1000, 10% v/w PEG 3500P. Heavy atom ...Details: Reservoir composition for crystal growth: 0.03M Magnesium chloride, 0.03 M calcium chloride, 0.05M imidazole, 0.05M MES, 10% v/v MPD, 10% w/v PEG 1000, 10% v/w PEG 3500P. Heavy atom derivatization: 1.2uL crystallization mother liquor containing 0.5mM KAu(CN)2 added to drop containing crystals. Drop size and composition: Sitting drops of 0.4ul were mixed in a protein:reservoir volume ratio of 1:1 using 45 mg/mL of OtCE15A in 20 mM TRIS pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→46.27 Å / Num. obs: 50802 / % possible obs: 95.9 % / Redundancy: 3.55 % / Biso Wilson estimate: 14.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.05 / Net I/σ(I): 16.69
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7975 / CC1/2: 0.923 / Rrim(I) all: 0.37 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot0.8.9 ELmodel building
XDSBUILT=20180126data reduction
PHENIX1.13_2998phasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure under deposition

Resolution: 1.5→46.27 Å / SU ML: 0.1099 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.0735
RfactorNum. reflection% reflection
Rfree0.1585 2101 4.14 %
Rwork0.1345 --
obs0.1355 50799 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 33 402 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833293
X-RAY DIFFRACTIONf_angle_d1.09284504
X-RAY DIFFRACTIONf_chiral_restr0.0764471
X-RAY DIFFRACTIONf_plane_restr0.0092603
X-RAY DIFFRACTIONf_dihedral_angle_d17.59421208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.24021340.1983095X-RAY DIFFRACTION91.71
1.53-1.570.22461360.17473162X-RAY DIFFRACTION94.63
1.57-1.610.17971380.16553205X-RAY DIFFRACTION94.81
1.61-1.660.20021390.15563217X-RAY DIFFRACTION94.86
1.66-1.720.17861390.15013228X-RAY DIFFRACTION95.25
1.72-1.780.16571390.14193223X-RAY DIFFRACTION95.7
1.78-1.850.1661400.13943242X-RAY DIFFRACTION95.92
1.85-1.930.18381400.14113246X-RAY DIFFRACTION96.11
1.93-2.030.17771410.13463266X-RAY DIFFRACTION96.41
2.03-2.160.1591410.13073258X-RAY DIFFRACTION96.89
2.16-2.330.1411430.12673321X-RAY DIFFRACTION97.52
2.33-2.560.1571420.12453291X-RAY DIFFRACTION97.45
2.56-2.930.14391430.1263311X-RAY DIFFRACTION97.71
2.93-3.70.15031420.12443309X-RAY DIFFRACTION98.15
3.7-46.290.14051440.13193324X-RAY DIFFRACTION98.47

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