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- PDB-1h54: Maltose phosphorylase from Lactobacillus brevis -

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Basic information

Entry
Database: PDB / ID: 1h54
TitleMaltose phosphorylase from Lactobacillus brevis
ComponentsMALTOSE PHOSPHORYLASE
KeywordsHYDROLASE / MALTOSE METABOLISM
Function / homology
Function and homology information


glycosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 ...Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycoside hydrolase family 65, N-terminal domain superfamily / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Hydrolase
Similarity search - Component
Biological speciesLACTOBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsVan Tilbeurgh, H. / Egloff, M.-P.
Citation
Journal: Structure / Year: 2001
Title: Crystal Structure of Maltose Phosphorylase from Lactobacillus Brevis: Unexpected Evolutionary Relationship with Glucoamylases.
Authors: Egloff, M.-P. / Uppenberg, J. / Haalck, L. / Van Tilbeurgh, H.
#1: Journal: Enzyme.Microb.Technol. / Year: 1997
Title: Maltose Phosphorylase from Lactobacillus Brevis: Purification, Characterization, and Application in a Biosensor for Ortho-Phosphate.
Authors: Huwel, S. / Haalck, L. / Conrath, N. / Spener, F.
History
DepositionMay 18, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: MALTOSE PHOSPHORYLASE
B: MALTOSE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8335
Polymers171,6592
Non-polymers1733
Water28,6801592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-11.7 kcal/mol
Surface area52820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.750, 102.500, 114.000
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MALTOSE PHOSPHORYLASE


Mass: 85829.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) LACTOBACILLUS BREVIS (bacteria) / References: UniProt: Q7SIE1*PLUS, EC: 2.4.1.8
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1592 / 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: 2.66 Å3/Da / Density % sol: 58 %
Crystal growpH: 6
Details: O.1 M CITRATE, 0.03M PHOSPHATE; PH 6.0, 20% POLY ACRYLIC ACID 20000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein1drop
210 mMcitrate1drop
318 %PAA200001reservoir
40.1 Mcitrate1reservoir
50.03 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.3
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 95868 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 11.1 Å2 / Rsym value: 0.076 / Net I/σ(I): 23
Reflection shellResolution: 2.15→2.35 Å / Mean I/σ(I) obs: 7.7 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.15→29.1 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5742 6 %RANDOM
Rwork0.186 ---
obs0.186 95793 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1 Å2 / ksol: 0.348419 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12100 0 7 1592 13699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 892 5.8 %
Rwork0.215 14545 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173 / Rfactor Rfree: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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