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

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Basic information

Entry
Database: PDB / ID: 4bzf
TitleCrystal structure of galactose mutarotase GalM from Bacillus subtilis with trehalose
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
trehalose / ACETATE ION / CITRIC ACID / TRIETHYLENE GLYCOL / Aldose 1-epimerase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 with Trehalose
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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
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)75,5658
Polymers74,2872
Non-polymers1,2786
Water11,728651
1
A: ALDOSE 1-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8284
Polymers37,1441
Non-polymers6853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALDOSE 1-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7374
Polymers37,1441
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.190, 83.322, 124.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2040-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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 (bacteria) / Strain: 168 / Gene: GALM / Plasmid: PET20B / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): KRX / References: UniProt: P39840, aldose 1-epimerase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 655 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.55 Å3/Da / Density % sol: 51.45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→37.16 Å / Num. obs: 67897 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

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

3mwx


Resolution: 1.9→37.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.187 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23773 3435 5.1 %RANDOM
Rwork0.19441 ---
obs0.19658 64415 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 86 651 5959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9527426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22424.791263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7281516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214144
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 226 -
Rwork0.326 4318 -
obs--96.95 %
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)
11.0410.0477-0.26521.7547-0.3271.7871-0.0038-0.00630.06510.0375-0.0028-0.22-0.06980.1750.00650.06710.0039-0.00230.1033-0.00210.09464.631320.673-17.4349
21.1240.6039-0.560.7478-0.37261.0371-0.01320.0227-0.0484-0.0470.0014-0.04850.06470.05050.01190.06880.0146-0.00390.0483-0.02250.066-11.03869.9218-11.3737
30.64780.2407-0.00620.84160.10030.5534-0.00850.0146-0.0024-0.01670.00210.0330.0055-0.02890.00630.05930.0209-0.0020.07260.01210.0848-13.573718.0233-7.5628
41.80660.8091-0.51561.6196-0.03310.9298-0.0324-0.16320.00930.15420.0049-0.095-0.03710.03010.02760.09820.00460.01110.0734-0.01760.0596-9.103828.62062.9887
50.69930.3088-0.05790.6364-0.01710.37840.00350.01090.0168-0.00090.00160.0146-0.00950.0068-0.00520.07530.01030.00790.0622-0.00520.0629-14.135821.1013-5.4881
69.67074.11864.62713.75812.36624.27650.014-0.78850.87940.589-0.1437-0.2915-0.57610.29810.12970.4526-0.1168-0.08970.3606-0.12120.37260.705536.7558-8.8233
71.1768-0.0274-0.25610.69820.24760.90850.01050.0487-0.036-0.0372-0.04670.1198-0.0107-0.12090.03620.1027-0.012-0.00860.08620.01450.07482.911517.7103-48.0976
81.542-0.9561-1.22831.30361.48142.5208-0.00590.0373-0.0659-0.066-0.0509-0.0320.0639-0.07480.05690.1066-0.0213-0.01130.09870.03760.11313.464110.3864-47.641
90.6992-0.1075-0.03760.74120.03010.8183-0.0025-0.043-0.04420.03430.0041-0.06510.0670.084-0.00170.0923-0.01950.00510.0977-0.00690.112714.172718.8607-48.811
101.2139-1.1235-0.18892.369-0.50390.92560.04650.12570.0233-0.1561-0.02460.0196-0.03640.0089-0.02190.1446-0.00630.00970.1525-0.00330.112115.863123.4758-69.2053
110.8668-0.3076-0.02740.79030.01980.52850.01380.03910.0072-0.0253-0.0109-0.02580.00690.0178-0.00280.1114-0.01220.01160.09670.00490.094214.926323.2292-56.9616
127.1418-5.41565.95615.3266-5.31886.6695-0.0450.42520.5148-0.2373-0.02530.2295-0.4279-0.31850.07020.40270.0909-0.10040.36970.09240.4158-0.783838.8787-56.0742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 53
2X-RAY DIFFRACTION2A54 - 125
3X-RAY DIFFRACTION3A126 - 219
4X-RAY DIFFRACTION4A220 - 251
5X-RAY DIFFRACTION5A252 - 318
6X-RAY DIFFRACTION6A319 - 323
7X-RAY DIFFRACTION7B2 - 84
8X-RAY DIFFRACTION8B85 - 119
9X-RAY DIFFRACTION9B120 - 200
10X-RAY DIFFRACTION10B201 - 240
11X-RAY DIFFRACTION11B241 - 318
12X-RAY DIFFRACTION12B319 - 324

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