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- PDB-4xuv: Crystal structure of a glycoside hydrolase family 105 (GH105) enz... -

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Basic information

Entry
Database: PDB / ID: 4xuv
TitleCrystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris
ComponentsGlycoside hydrolase family 105 protein
KeywordsHYDROLASE / GH105 / glycoside hydrolase / fungus / genomics / alpha6/alpha6-barrel
Function / homology
Function and homology information


carbohydrate metabolic process / hydrolase activity
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 105 protein
Similarity search - Component
Biological speciesThielavia terrestris (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.0496 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Yim, V. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris
Authors: Stogios, P.J. / Xu, X. / Cui, H. / Yim, V. / Savchenko, A.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 105 protein
B: Glycoside hydrolase family 105 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3565
Polymers84,0802
Non-polymers2763
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-17 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.258, 126.258, 117.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Glycoside hydrolase family 105 protein


Mass: 42039.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (strain ATCC 38088 / NRRL 8126) (fungus)
Strain: ATCC 38088 / NRRL 8126 / Gene: THITE_2110935 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G2QVG2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M potassium/sodium phosphate, trypsin protease cryo: 12% (w/v) glycerol then paratone-N oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.0496→30 Å / Num. obs: 57560 / % possible obs: 100 % / Redundancy: 8.2 % / Rsym value: 0.048 / Net I/σ(I): 16.86
Reflection shellResolution: 2.0496→2.09 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.278 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PMM, 1NC5

3pmm

1nc5


Resolution: 2.0496→29.759 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1982 3.47 %Random selection
Rwork0.191 ---
obs0.1921 57103 99.14 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0496→29.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5279 0 18 554 5851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025445
X-RAY DIFFRACTIONf_angle_d0.6627394
X-RAY DIFFRACTIONf_dihedral_angle_d14.4841908
X-RAY DIFFRACTIONf_chiral_restr0.024788
X-RAY DIFFRACTIONf_plane_restr0.003940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0496-2.10080.25321390.21123844X-RAY DIFFRACTION97
2.1008-2.15760.23131390.20793827X-RAY DIFFRACTION98
2.1576-2.22110.21551350.20393945X-RAY DIFFRACTION99
2.2211-2.29270.23311340.20043926X-RAY DIFFRACTION99
2.2927-2.37460.26021540.20063892X-RAY DIFFRACTION99
2.3746-2.46970.22941440.19753897X-RAY DIFFRACTION99
2.4697-2.5820.25231340.19623929X-RAY DIFFRACTION99
2.582-2.71810.22971480.20183940X-RAY DIFFRACTION99
2.7181-2.88820.21031390.19424002X-RAY DIFFRACTION100
2.8882-3.1110.24591420.1973930X-RAY DIFFRACTION100
3.111-3.42370.21871390.19173976X-RAY DIFFRACTION100
3.4237-3.91810.21241390.17523986X-RAY DIFFRACTION100
3.9181-4.93280.18131390.16753990X-RAY DIFFRACTION100
4.9328-29.76240.22921570.20164037X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5451-1.1489-0.47963.10110.28822.29890.08310.3786-0.0752-0.427-0.04730.20620.051-0.1545-0.03870.26950.0276-0.00880.29-0.04640.1635-6.8906-25.1531-29.6251
21.2483-0.5056-0.03511.8628-0.99841.9447-0.0148-0.0588-0.1204-0.07140.03650.1940.1117-0.2176-0.01660.1299-0.015-0.00480.1662-0.03490.1489-18.1493-24.9771-10.2796
31.8317-0.5305-0.38263.02840.53612.5745-0.04180.0675-0.4109-0.0539-0.06670.07170.4234-0.08250.06470.1957-0.03850.04360.1923-0.00080.2692-4.3021-36.0314-9.2506
41.58710.101-0.20232.9381-0.56253.0834-0.07260.2659-0.4325-0.2608-0.0497-0.16410.3668-0.0260.05980.20940.0260.05450.2239-0.06840.3026-0.201-37.4918-20.5053
55.2526-2.7830.18457.357-0.78395.29510.1245-1.0508-0.04430.8032-0.08880.2552-0.2072-0.5642-0.0780.3766-0.11460.1020.420.05120.2211-22.1371-23.585139.5962
62.5389-0.5304-0.44551.72510.56581.8153-0.0112-0.41690.00140.29130.0406-0.08180.15910.0148-0.03530.2043-0.0161-0.01980.25550.04960.1594-1.7374-23.573230.727
71.99610.67950.56851.53650.98152.57970.1139-0.0854-0.33830.2705-0.0962-0.09950.4269-0.0085-0.02780.20940.024-0.00010.15680.04830.18-4.5944-35.143613.3151
81.92080.9722-0.70682.6214-0.2261.96320.0252-0.1417-0.1160.2008-0.10750.16230.1375-0.1490.08190.16380.00370.03420.19180.02260.1924-21.5528-29.735122.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:92)
2X-RAY DIFFRACTION2(chain A and resid 93:218)
3X-RAY DIFFRACTION3(chain A and resid 219:283)
4X-RAY DIFFRACTION4(chain A and resid 284:378)
5X-RAY DIFFRACTION5(chain B and resid 8:24)
6X-RAY DIFFRACTION6(chain B and resid 25:134)
7X-RAY DIFFRACTION7(chain B and resid 135:220)
8X-RAY DIFFRACTION8(chain B and resid 221:378)

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