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- PDB-2x1i: glycoside hydrolase family 77 4-alpha-glucanotransferase from the... -

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Basic information

Entry
Database: PDB / ID: 2x1i
Titleglycoside hydrolase family 77 4-alpha-glucanotransferase from thermus brockianus
Components4-ALPHA-GLUCANOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / PHOSPHATE ION / 4-alpha-glucanotransferase
Similarity search - Component
Biological speciesTHERMUS BROCKIANUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsYoon, S.-M. / Jung, J.-H. / Jung, T.-Y. / Song, H.-N. / Park, C.-S. / Woo, E.-J.
CitationJournal: Proteins / Year: 2011
Title: Structural and Functional Analysis of Substrate Recognition by the 250S Loop in Amylomaltase from Thermus Brockianus.
Authors: Jung, J.-H. / Jung, T.-Y. / Seo, D. / Yoon, S.-M. / Choi, H. / Park, B.C. / Park, C.-S. / Woo, E.-J.
History
DepositionDec 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: 4-ALPHA-GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9055
Polymers57,3541
Non-polymers5514
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.357, 104.357, 263.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 4-ALPHA-GLUCANOTRANSFERASE / / AMYLOMALTASE


Mass: 57353.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS BROCKIANUS (bacteria) / Strain: JCM11602 / References: UniProt: Q2VJA0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.57 Å3/Da / Density % sol: 65.61 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M BIS-TRIS PH6.5, 45% PPGP400, 12% INOSITOL(ADDITIVE)

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.36→29.93 Å / Num. obs: 35592 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 34.06
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.36 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.2refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OWC

2owc


Resolution: 2.36→29.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 76946.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1512 4.2 %RANDOM
Rwork0.215 ---
obs0.215 35592 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5482 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---1.53 Å20 Å2
3---3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.36→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 34 110 4189
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.312.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 14 0.2 %
Rwork0.281 5587 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4INS_XPLOR_PAR.TXTINS_XPLOR_TOP.TXT

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