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- PDB-2okx: Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1... -

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Basic information

Entry
Database: PDB / ID: 2okx
TitleCrystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A
ComponentsRhamnosidase B
KeywordsHYDROLASE / alpha barrel / rhamnosidase / glycoside hydrolase family 78 / invertase
Function / homology
Function and homology information


alpha-L-rhamnosidase / alpha-L-rhamnosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Bacterial alpha-L-rhamnosidase N-terminal / Alpha-L-rhamnosidase N-terminal domain / Alpha-L-rhamnosidase, concanavalin-like domain / Bacterial alpha-L-rhamnosidase concanavalin-like domain / Alpha-L-rhamnosidase C-terminal domain / Bacterial alpha-L-rhamnosidase C-terminal domain / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 ...Bacterial alpha-L-rhamnosidase N-terminal / Alpha-L-rhamnosidase N-terminal domain / Alpha-L-rhamnosidase, concanavalin-like domain / Bacterial alpha-L-rhamnosidase concanavalin-like domain / Alpha-L-rhamnosidase C-terminal domain / Bacterial alpha-L-rhamnosidase C-terminal domain / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Alpha-L-rhamnosidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.9 Å
AuthorsCui, Z. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Glycoside Hydrolase Family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1
Authors: Cui, Z. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Rhamnosidase B
B: Rhamnosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,42849
Polymers212,3082
Non-polymers4,12047
Water31,6161755
1
A: Rhamnosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,16824
Polymers106,1541
Non-polymers2,01423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhamnosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,26025
Polymers106,1541
Non-polymers2,10624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-68 kcal/mol
Surface area60490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.744, 119.985, 207.352
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 Rhamnosidase B


Mass: 106153.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Gene: rhaB / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93RE7, alpha-L-rhamnosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1755 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13.5%(W/V) PEG 8000, 0.08M sodium cacodylate, 0.16M calcium acetate, 20%(V/V) glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B111
SYNCHROTRONSPring-8 BL38B120.97916
Detector
TypeIDDetectorDateDetails
RIGAKU JUPITER 2101CCDMar 20, 2006MIRRORS
RIGAKU JUPITER 2102CCDMar 15, 2005MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SILSINGLE WAVELENGTHMx-ray1
2SILSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979161
ReflectionResolution: 1.9→49.4 Å / Num. obs: 188971 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.1 / % possible all: 91

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.78 / FOM acentric: 0.79 / FOM centric: 0.74 / Reflection: 80307 / Reflection acentric: 73605 / Reflection centric: 6702
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.3-103.8420.880.90.8237432922821
4.5-7.30.870.880.81091396161297
3.6-4.50.880.880.8213562123591203
3.2-3.60.820.830.7513610125811029
2.7-3.20.730.730.6824057224761581
2.5-2.70.650.650.581442213651771

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.06phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: SAD MODEL

Resolution: 1.9→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3179334.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.214 18716 9.9 %RANDOM
Rwork0.182 ---
obs0.182 188458 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.06 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å20 Å2
2---3.69 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14954 0 262 1755 16971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 2876 9.9 %
Rwork0.253 26036 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAMACT.TOP
X-RAY DIFFRACTION5GOL.PARAMGOL.TOP

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