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- PDB-4nzf: Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase fr... -

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Basic information

Entry
Database: PDB / ID: 4nzf
TitleCrystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus), in complex with arabinose
ComponentsAbp, a GH27 beta-L-arabinopyranosidase
KeywordsHYDROLASE / Tim Barrel / Glycoside Hydrolase
Function / homology
Function and homology information


Golgi alpha-mannosidase II / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-L-arabinopyranose / CITRIC ACID
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLansky, S. / Solomon, H.V. / Salama, R. / Belrhali, H. / Shoham, Y. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure-specificity relationships in Abp, a GH27 beta-L-arabinopyranosidase from Geobacillus stearothermophilus T6
Authors: Lansky, S. / Salama, R. / Solomon, H.V. / Feinberg, H. / Belrhali, H. / Shoham, Y. / Shoham, G.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abp, a GH27 beta-L-arabinopyranosidase
B: Abp, a GH27 beta-L-arabinopyranosidase
C: Abp, a GH27 beta-L-arabinopyranosidase
D: Abp, a GH27 beta-L-arabinopyranosidase
E: Abp, a GH27 beta-L-arabinopyranosidase
F: Abp, a GH27 beta-L-arabinopyranosidase
G: Abp, a GH27 beta-L-arabinopyranosidase
H: Abp, a GH27 beta-L-arabinopyranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,650124
Polymers409,5778
Non-polymers12,073116
Water52,8202932
1
A: Abp, a GH27 beta-L-arabinopyranosidase
B: Abp, a GH27 beta-L-arabinopyranosidase
C: Abp, a GH27 beta-L-arabinopyranosidase
D: Abp, a GH27 beta-L-arabinopyranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,87472
Polymers204,7894
Non-polymers7,08568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-561 kcal/mol
Surface area60190 Å2
MethodPISA
2
E: Abp, a GH27 beta-L-arabinopyranosidase
F: Abp, a GH27 beta-L-arabinopyranosidase
G: Abp, a GH27 beta-L-arabinopyranosidase
H: Abp, a GH27 beta-L-arabinopyranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,77652
Polymers204,7894
Non-polymers4,98848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-430 kcal/mol
Surface area59240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.600, 201.505, 286.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Abp, a GH27 beta-L-arabinopyranosidase


Mass: 51197.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-ARB / beta-L-arabinopyranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinopyranoseCOMMON NAMEGMML 1.0
b-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 3040 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 82 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2932 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE UNP SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS PROTEIN IS D197A MUTANT.

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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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8M Ammonium Sulfate, 0.1M citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.19→34.71 Å / Num. all: 301393 / Num. obs: 268240 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.19→2.25 Å / % possible all: 76.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NXK

4nxk


Resolution: 2.19→34.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.544 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21888 14318 5.1 %RANDOM
Rwork0.16847 ---
obs0.17098 268240 89.04 %-
all-301393 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.962 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0 Å20 Å2
2--2.96 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.19→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27794 0 688 2932 31414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01929299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0226767
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.95539815
X-RAY DIFFRACTIONr_angle_other_deg0.948361610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52753474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58423.7631398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.634154751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.75715176
X-RAY DIFFRACTIONr_chiral_restr0.1260.24165
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02132723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026977
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3473.27513827
X-RAY DIFFRACTIONr_mcbond_other3.3463.27513826
X-RAY DIFFRACTIONr_mcangle_it4.8954.89417279
X-RAY DIFFRACTIONr_mcangle_other4.8954.89417280
X-RAY DIFFRACTIONr_scbond_it3.9473.64615472
X-RAY DIFFRACTIONr_scbond_other3.9223.63815452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.85.32622492
X-RAY DIFFRACTIONr_long_range_B_refined8.5927.3638186
X-RAY DIFFRACTIONr_long_range_B_other8.57627.34438157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.194→2.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 895 -
Rwork0.247 16966 -
obs--76.74 %

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