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- PDB-4bzg: Crystal structure of galactose mutarotase GalM from Bacillus subt... -

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Basic information

Entry
Database: PDB / ID: 4bzg
TitleCrystal structure of galactose mutarotase GalM from Bacillus subtilis in complex with maltose
ComponentsALDOSE 1-EPIMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


aldose 1-epimerase / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / cytoplasm
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / CITRIC ACID / Aldose 1-epimerase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsVanden Broeck, A. / Sauvage, E. / Herman, R. / Kerff, F. / Duez, C. / Charlier, P.
CitationJournal: To be Published
Title: Crystal Structure of Galactose Mutarotase Galm from Bacillus Subtilis in Complex with Maltose
Authors: Vanden Broeck, A. / Sauvage, E. / Herman, R. / Kerff, F. / Duez, C. / Charlier, P.
History
DepositionJul 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDOSE 1-EPIMERASE
B: ALDOSE 1-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1645
Polymers74,2872
Non-polymers8773
Water5,657314
1
A: ALDOSE 1-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4862
Polymers37,1441
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALDOSE 1-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6783
Polymers37,1441
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.461, 84.202, 125.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALDOSE 1-EPIMERASE / GALACTOSE MUTAROTASE


Mass: 37143.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Gene: GALM / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): KRX / References: UniProt: P39840, aldose 1-epimerase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.78 Å3/Da / Density % sol: 55.41 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→29.67 Å / Num. obs: 49195 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2
Reflection shellResolution: 2.13→2.24 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.4 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MWX

3mwx


Resolution: 2.13→29.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.015 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22671 2457 5 %RANDOM
Rwork0.18284 ---
obs0.18504 46673 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.13→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 59 314 5595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.025431
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9487398
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92824.791263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53915891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2431516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.125→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 136 -
Rwork0.3 2579 -
obs--78.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53650.189-0.09330.6533-0.13680.49190.0390.0336-0.101-0.0427-0.0232-0.10310.00890.0841-0.01580.07680.02240.01490.0368-0.00560.1362-1.76316.229-13.749
20.65330.3475-0.31450.5621-0.16290.43480.01580.1183-0.1253-0.07280.0024-0.05210.0365-0.005-0.01820.10330.0176-0.00210.0495-0.01730.1194-12.11411.063-16.593
30.7099-0.01340.04940.53620.12670.47-0.0059-0.03090.03190.03620.00730.03730.03350.0005-0.00140.08330.00680.00750.0420.01020.0971-13.35821.489-2.266
42.8548-1.091-0.05371.737-0.32930.69110.1631-0.22640.09420.1083-0.11170.0548-0.04330.0164-0.05140.0891-0.00410.01470.0733-0.01020.0683-11.36127.7694.467
50.66540.0722-0.13610.34780.12430.31160.0102-0.0112-0.016-0.0062-0.0097-0.0118-0.0164-0.0097-0.00050.08150.00640.00320.04980.01470.1264-12.90522.58-5.16
627.00513.640616.338815.20280.208217.671-0.13731.67910.74350.40910.26310.9937-0.56311.6037-0.12590.1435-0.04880.14130.1742-0.04160.23260.54937.014-9.444
70.07010.3115-0.02671.88950.48082.2958-0.02480.04620.00940.0310.01020.1687-0.0113-0.2850.01460.0836-0.02890.05280.1564-0.01450.0715-3.26122.983-45.317
83.17660.065-1.44360.52170.01260.6762-0.23950.1075-0.1779-0.14940.1198-0.05220.1584-0.04340.11970.2922-0.00970.13170.084-0.05170.105712.8219.594-53.559
90.4463-0.0416-0.81861.68040.41621.5753-0.27710.2023-0.1497-0.26480.0628-0.34670.4402-0.37340.21430.3063-0.07080.12930.1601-0.11010.138116.6244.007-55.848
100.8932-1.0549-1.52622.90631.71514.5154-0.0925-0.1744-0.0890.05820.1397-0.0148-0.08980.1872-0.04720.1061-0.01950.03630.09310.02910.05656.32222.602-36.984
110.8718-0.1955-0.15670.9773-0.23360.3413-0.06630.11350.0255-0.13680.0001-0.14970.0661-0.02170.06620.1282-0.00590.06090.1303-0.00730.042314.68621.636-57.117
1238.26596.450630.11331.08865.078623.7021-3.027-0.83953.7227-0.5078-0.02650.6365-2.4275-0.64353.05350.72180.1094-0.12950.1623-0.04020.4331-1.90440.159-57.286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 85
2X-RAY DIFFRACTION2A86 - 153
3X-RAY DIFFRACTION3A154 - 219
4X-RAY DIFFRACTION4A220 - 243
5X-RAY DIFFRACTION5A244 - 318
6X-RAY DIFFRACTION6A319 - 323
7X-RAY DIFFRACTION7B2 - 52
8X-RAY DIFFRACTION8B53 - 85
9X-RAY DIFFRACTION9B86 - 105
10X-RAY DIFFRACTION10B106 - 124
11X-RAY DIFFRACTION11B125 - 319
12X-RAY DIFFRACTION12B320 - 324

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