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- PDB-3w0k: Crystal Structure of a glycoside hydrolase -

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Basic information

Entry
Database: PDB / ID: 3w0k
TitleCrystal Structure of a glycoside hydrolase
ComponentsBifunctional endomannanase/endoglucanase
KeywordsHYDROLASE / Beta/Alpha barrel
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaldanaerobius polysaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOyama, T. / Nakamura, H. / Morikawa, K. / Cann, I.K.O.
CitationJournal: To be Published
Title: Crystal structure of a glycoside hydrolase
Authors: Oyama, T. / Schmitz, G.E. / Dodd, D. / Han, Y. / Burnett, A. / Nagasawa, N. / Mackie, R.I. / Nakamura, H. / Morikawa, K. / Cann, I.K.O.
History
DepositionOct 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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: Bifunctional endomannanase/endoglucanase
B: Bifunctional endomannanase/endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7254
Polymers78,4812
Non-polymers2442
Water11,277626
1
A: Bifunctional endomannanase/endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3632
Polymers39,2401
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional endomannanase/endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3632
Polymers39,2401
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.133, 147.642, 55.422
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional endomannanase/endoglucanase / beta-mannnanase/endoglucanase


Mass: 39240.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobius polysaccharolyticus (bacteria)
Gene: man5B / Plasmid: pET46b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9J0D7
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 50%(v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: FIXED EXIT SI 111 DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 102028 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.036

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VJZ

1vjz


Resolution: 1.6→19.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 146422.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.188 5070 5.1 %RANDOM
Rwork0.176 ---
obs0.176 100324 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.321 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å2-2 Å2
2---3.16 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 16 626 6099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.422.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 845 5.2 %
Rwork0.216 15252 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3trs_xplor_param.txttrs_xplor_top.txt

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