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- PDB-3r4y: Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) f... -

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Basic information

Entry
Database: PDB / ID: 3r4y
TitleCrystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) from Saccharophagus degradans 2-40
ComponentsGlycosyl hydrolase family 32, N terminal
KeywordsHYDROLASE / AGAR METABOLISM / NEOAGAROBIOSE / 3 / 6-ANHYDRO-L-GALACTOSE / BIOENERGY
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Single helix bin / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Glycosyl hydrolase family 32, N terminal
Similarity search - Component
Biological speciesSaccharophagus degradans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLee, S. / Lee, J.Y. / Ha, S.C. / Shin, D.H. / Kim, K.H. / Bang, W.G. / Kim, S.H. / Choi, I.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of a key enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus degradans 2-40
Authors: Ha, S.C. / Lee, S. / Lee, J. / Kim, H.T. / Ko, H.J. / Kim, K.H. / Choi, I.G.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 32, N terminal
B: Glycosyl hydrolase family 32, N terminal


Theoretical massNumber of molelcules
Total (without water)84,8802
Polymers84,8802
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-35 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.87, 76.81, 90.11
Angle α, β, γ (deg.)90.00, 101.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-421-

HOH

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Components

#1: Protein Glycosyl hydrolase family 32, N terminal / ALPHA-NEOAGAROBIOSE HYDROLASE


Mass: 42439.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharophagus degradans (bacteria) / Strain: 2-40 / Gene: Sde_2657 / Plasmid: PJL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q21HB2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2009
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 55856 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.3
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.279 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2710 5.1 %RANDOM
Rwork0.161 ---
obs0.164 50502 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.03 Å2
2---0.01 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 0 303 6058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225935
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9318060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97724.141297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7591528
X-RAY DIFFRACTIONr_chiral_restr0.1190.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024684
X-RAY DIFFRACTIONr_nbd_refined0.2070.22665
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2456
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.29
X-RAY DIFFRACTIONr_mcbond_it1.2261.53645
X-RAY DIFFRACTIONr_mcangle_it1.97725734
X-RAY DIFFRACTIONr_scbond_it3.11232683
X-RAY DIFFRACTIONr_scangle_it4.7254.52326
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 158 -
Rwork0.17 3331 -
obs--100 %

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