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- PDB-4wvc: Crystal structure of GH63 mannosylglycerate hydrolase from Thermu... -

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Basic information

Entry
Database: PDB / ID: 4wvc
TitleCrystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with Tris and D-glycerate
ComponentsUncharacterized protein
KeywordsHYDROLASE / GH63 / (alpha/alpha)6-barrel
Function / homology
Function and homology information


trehalose metabolic process / alpha,alpha-trehalase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / protein N-linked glycosylation
Similarity search - Function
Glycoside hydrolase, family 37 / Trehalase / Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-DIHYDROXYPROPANOIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMiyazaki, T. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8.
Authors: Miyazaki, T. / Ichikawa, M. / Iino, H. / Nishikawa, A. / Tonozuka, T.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2068
Polymers97,6782
Non-polymers5276
Water4,774265
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,30812
Polymers146,5173
Non-polymers7919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9200 Å2
ΔGint-7 kcal/mol
Surface area39090 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,30812
Polymers146,5173
Non-polymers7919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9580 Å2
ΔGint-7 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.940, 92.940, 190.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-500-

CL

21B-500-

CL

31A-621-

HOH

41A-633-

HOH

51A-640-

HOH

61B-638-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 48839.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0978 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJN0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-DGY / (2R)-2,3-DIHYDROXYPROPANOIC ACID


Mass: 106.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4M potassium sodium tartrate, 0.1M HEPES-NaOH (pH 7.5), 50mM calcium chloride, 10mM D-glycerate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 55067 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.5 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata processing
SCALAdata scaling
MOLREPphasing
Cootmodel building
SCALEPACKdata reduction
RefinementResolution: 2.1→45.145 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.825 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27971 2809 5.1 %RANDOM
Rwork0.24472 ---
obs0.24653 52252 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.159 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 32 265 7093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197058
X-RAY DIFFRACTIONr_bond_other_d00.026467
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9479620
X-RAY DIFFRACTIONr_angle_other_deg3.556314801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78722.016372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.946151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8271579
X-RAY DIFFRACTIONr_chiral_restr0.1280.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218007
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021824
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_it1.6092.9233286
X-RAY DIFFRACTIONr_mcbond_other1.6092.9223284
X-RAY DIFFRACTIONr_mcangle_it2.5154.3784098
X-RAY DIFFRACTIONr_mcangle_other2.5154.3784099
X-RAY DIFFRACTIONr_scbond_it1.6783.1113772
X-RAY DIFFRACTIONr_scbond_other1.6773.1113772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7314.65522
X-RAY DIFFRACTIONr_long_range_B_refined4.90924.0888688
X-RAY DIFFRACTIONr_long_range_B_other4.88324.0868628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 199 -
Rwork0.296 3662 -
obs--93.6 %

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