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- PDB-4qqs: Crystal structure of a thermostable family-43 glycoside hydrolase -

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Basic information

Entry
Database: PDB / ID: 4qqs
TitleCrystal structure of a thermostable family-43 glycoside hydrolase
ComponentsGlycoside hydrolase family 43
KeywordsHYDROLASE / 5-bladed beta-propeller / glycoside hydrolase
Function / homology
Function and homology information


xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase family 43
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHassan, N. / Kori, L.D. / Patel, B.K.C. / Divne, C. / Tan, T.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with alpha-L-arabinofuranosidase activity.
Authors: Hassan, N. / Kori, L.D. / Gandini, R. / Patel, B.K. / Divne, C. / Tan, T.C.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 43
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9007
Polymers71,1392
Non-polymers7615
Water18,5911032
1
A: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0694
Polymers35,5701
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8313
Polymers35,5701
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.133, 73.882, 87.520
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoside hydrolase family 43


Mass: 35569.711 Da / Num. of mol.: 2 / Fragment: glycoside hydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / OCM 544 / DSM 9562 / Gene: Hore_20580 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8CZV1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / pH: 6.2
Details: 0.1 M Hepes pH 6.2, 0.16 M potassium thiocyanate and 25% (w/v) polyethylene glycol 3350, 0.15 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→44.011 Å / Num. obs: 213964 / % possible obs: 94.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 7.7 / Rsym value: 0.224 / % possible all: 89.3

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KST

3kst


Resolution: 1.1→44.01 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 13.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.145 1990 0.93 %
Rwork0.122 --
obs0.123 213960 94.5 %
all-213960 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 47 1032 6069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095263
X-RAY DIFFRACTIONf_angle_d1.3297172
X-RAY DIFFRACTIONf_dihedral_angle_d14.4121936
X-RAY DIFFRACTIONf_chiral_restr0.084722
X-RAY DIFFRACTIONf_plane_restr0.007926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12750.18421180.146713785X-RAY DIFFRACTION86
1.1275-1.1580.17161550.13114403X-RAY DIFFRACTION90
1.158-1.19210.13941280.120514573X-RAY DIFFRACTION91
1.1921-1.23060.12251400.115814723X-RAY DIFFRACTION92
1.2306-1.27450.15131360.114914936X-RAY DIFFRACTION94
1.2745-1.32560.13481440.110915066X-RAY DIFFRACTION94
1.3256-1.38590.13961420.111415169X-RAY DIFFRACTION95
1.3859-1.4590.1311540.10415222X-RAY DIFFRACTION95
1.459-1.55040.12451300.100715362X-RAY DIFFRACTION96
1.5504-1.67010.13361510.102815452X-RAY DIFFRACTION97
1.6701-1.83820.12671420.110315631X-RAY DIFFRACTION97
1.8382-2.10420.11681430.114115706X-RAY DIFFRACTION98
2.1042-2.6510.14321550.13515837X-RAY DIFFRACTION98
2.651-44.0460.17281520.134816105X-RAY DIFFRACTION99

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