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- PDB-1bpl: GLYCOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1bpl
TitleGLYCOSYLTRANSFERASE
Components(ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE) x 2
KeywordsGLYCOSYLTRANSFERASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Transcription Regulator spoIIAA - #90 / Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Transcription Regulator spoIIAA / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Transcription Regulator spoIIAA - #90 / Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Transcription Regulator spoIIAA / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMachius, M. / Wiegand, G. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
Authors: Machius, M. / Wiegand, G. / Huber, R.
History
DepositionJul 13, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
B: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)55,3162
Polymers55,3162
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-30 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.800, 119.800, 85.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE (BLA)


Mass: 21807.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P06278, alpha-amylase
#2: Protein ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE (BLA)


Mass: 33508.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P06278, alpha-amylase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE ...THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION. WITHOUT THIS CLEAVAGE, BLA DID NOT CRYSTALLIZE UNDER THE CONDITIONS APPLIED. DUE TO THIS CLEAVAGE, THE REGION BETWEEN TRP 182 AND ASN 192 IS NOT VISIBLE IN THE ELECTRON DENSITY. IN ADDITION THE FIRST TWO (N TERMINAL) RESIDUES ALA 1 AND ASN 2 AS WELL AS THE C-TERMINAL ARG 483 ARE NOT VISIBLE. A RAMACHANDRAN PLOT SHOWS THAT TYR 150, WHICH IS WELL DEFINED IN THE DENSITY, IS IN THE DISALLOWED REGION. ARG 134 HAS BEEN MODELED AS LEU AS THIS FITS BETTER INTO THE ELECTRON DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion / pH: 8.2
Details: MOLECULE: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE FROM BACILLUS LICHENIFORMIS. VAPOR DIFFUSION, ROOM TEMPERATURE PROTEIN SOLUTION: 15 MG/ML BLA IN 0.4 M SODIUM CITRATE 2.5 MM EDTA, PH 8.2 ...Details: MOLECULE: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE FROM BACILLUS LICHENIFORMIS. VAPOR DIFFUSION, ROOM TEMPERATURE PROTEIN SOLUTION: 15 MG/ML BLA IN 0.4 M SODIUM CITRATE 2.5 MM EDTA, PH 8.2 RESERVOIR: 0.66 M SODIUM CITRATE, 2.5 MM EDTA, PH 8.2 CALCIUM REMOVAL BY EDTA LEADS TO A CLEAVAGE OF BLA AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION (SEE PAPER)., vapor diffusion
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.4 Msodium citrate1drop
22.5 mMEDTA1drop
315 mg/mlBLA1drop
40.60-0.69 Msodium citrate1reservoir
52.5 mMEDTA1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 0
Details: THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION. WITHOUT THIS CLEAVAGE, BLA DID NOT CRYSTALLIZE UNDER THE ...Details: THE CALCIUM FREE FORM OF BLA IS CLEAVED AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION. WITHOUT THIS CLEAVAGE, BLA DID NOT CRYSTALLIZE UNDER THE CONDITIONS APPLIED. DUE TO THIS CLEAVAGE, THE REGION BETWEEN TRP 182 AND ASN 192 IS NOT VISIBLE IN THE ELECTRON DENSITY. IN ADDITION THE FIRST TWO (N TERMINAL) RESIDUES ALA 1 AND ASN 2 AS WELL AS THE C-TERMINAL ARG 483 ARE NOT VISIBLE. A RAMACHANDRAN PLOT SHOWS THAT TYR 150, WHICH IS WELL DEFINED IN THE DENSITY, IS IN THE DISALLOWED REGION. ARG 134 HAS BEEN MODELED AS LEU AS THIS FITS BETTER INTO THE ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 28093 89.7 %
Displacement parametersBiso mean: 20.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 0 237 4270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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