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- PDB-6cc7: Structure of Fungal GH62 from Thielavia terretris -

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Basic information

Entry
Database: PDB / ID: 6cc7
TitleStructure of Fungal GH62 from Thielavia terretris
ComponentsGlycoside hydrolase family 62 protein
KeywordsHYDROLASE / GH62 / glycoside hydrolase / domain swapping / Thielavia terrestris
Function / homologyGlycoside hydrolase, family 62, arabinosidase / Glycosyl hydrolase family 62 / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / xylan catabolic process / extracellular region / Non-reducing end alpha-L-arabinofuranosidase
Function and homology information
Biological speciesThielavia terrestris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsCamargo, S. / Mulinari, E.J. / Almeida, L.R. / Muniz, J.R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/16291-5 Brazil
Conselho Nacional de Desenvolvimento Cientifico e Tecnologico309767/2015-6 Brazil
CitationJournal: To Be Published
Title: Structure of Fungal GH62 from Thielavia terretris
Authors: Camargo, S. / Mulinari, E.J. / Almeida, L.R. / Muniz, J.R.C.
History
DepositionFeb 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 62 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0965
Polymers34,8021
Non-polymers2944
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.267, 79.747, 82.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21A-692-

HOH

31A-699-

HOH

41A-768-

HOH

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Components

#1: Protein Glycoside hydrolase family 62 protein


Mass: 34801.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (fungus) / Strain: ATCC 38088 / NRRL 8126 / Gene: THITE_2110954 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QVH2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1.89 Å3/Da / Density % sol: 31.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45863 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45863 Å / Relative weight: 1
ReflectionResolution: 1.87→57.48 Å / Num. obs: 20946 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1318 / CC1/2: 0.838 / Rpim(I) all: 0.349 / Rrim(I) all: 0.522 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o8n

4o8n


Resolution: 1.87→57.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.634 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 1178 5.6 %RANDOM
Rwork0.14736 ---
obs0.15019 19767 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 1.87→57.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 15 298 2619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022420
X-RAY DIFFRACTIONr_bond_other_d0.0020.022072
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9333306
X-RAY DIFFRACTIONr_angle_other_deg0.98134849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7445315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45824.356101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.43158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
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_it1.1232.0691229
X-RAY DIFFRACTIONr_mcbond_other1.1132.0661228
X-RAY DIFFRACTIONr_mcangle_it1.8363.0961538
X-RAY DIFFRACTIONr_mcangle_other1.8383.0991539
X-RAY DIFFRACTIONr_scbond_it1.1522.131190
X-RAY DIFFRACTIONr_scbond_other1.1522.131190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7683.161760
X-RAY DIFFRACTIONr_long_range_B_refined4.68825.2432813
X-RAY DIFFRACTIONr_long_range_B_other4.50924.7082757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 59 -
Rwork0.225 1461 -
obs--97.25 %
Refinement TLS params.Method: refined / Origin x: 24.045 Å / Origin y: 24.9745 Å / Origin z: 2.8268 Å
111213212223313233
T0.0218 Å2-0.0069 Å2-0.0132 Å2-0.0156 Å20.0044 Å2--0.0192 Å2
L0.4237 °2-0.0022 °2-0.151 °2-0.0051 °2-0.0157 °2--0.1824 °2
S0.0234 Å °0.0232 Å °-0.0236 Å °-0.0041 Å °0.0098 Å °0.0036 Å °0.0246 Å °-0.0347 Å °-0.0332 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 98
2X-RAY DIFFRACTION1A99 - 152
3X-RAY DIFFRACTION1A153 - 302
4X-RAY DIFFRACTION1A303 - 331

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