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- PDB-2rdy: Crystal structure of a putative glycoside hydrolase family protei... -

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Basic information

Entry
Database: PDB / ID: 2rdy
TitleCrystal structure of a putative glycoside hydrolase family protein from Bacillus halodurans
ComponentsBH0842 protein
KeywordsHYDROLASE / 10436a / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


alpha-L-fucosidase activity / carbohydrate metabolic process
Similarity search - Function
Alpha-L-fucosidase / : / : / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95 catalytic domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / putative glycoside hydrolase family protein from bacillus halodurans / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily ...Alpha-L-fucosidase / : / : / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95 catalytic domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / putative glycoside hydrolase family protein from bacillus halodurans / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative glycoside hydrolase family protein from Bacillus halodurans.
Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: BH0842 protein
B: BH0842 protein


Theoretical massNumber of molelcules
Total (without water)182,3912
Polymers182,3912
Non-polymers00
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.610, 149.071, 164.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH0842 protein


Mass: 91195.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: BH0842 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KEL0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 30% PEG 4000, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2007 / Details: Mirror
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 116075 / Num. obs: 116075 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 2.03→2.12 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2 / % possible all: 86.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
WARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.03→47.57 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 83205.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 6793 6 %RANDOM
Rwork0.198 ---
obs0.198 112521 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2113 Å2 / ksol: 0.401907 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---3.11 Å20 Å2
3---2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.03→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12480 0 0 559 13039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 996 6 %
Rwork0.209 15492 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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