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- PDB-4zfm: Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 4zfm
TitleStructure of Gan1D-E170Q in complex with cellobiose-6-phosphate
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / Cellobiose-6-phosphate / TIM barrel / catalytic mutant
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,5-anhydro-6-O-phosphono-D-glucitol / 6-O-phosphono-beta-D-glucopyranose / beta-D-glucopyranose / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Structure of Gan1D-E170Q in complex with cellobiose-6-phosphate
Authors: Lansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.title / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 6-phospho-beta-galactobiosidase
B: Putative 6-phospho-beta-galactobiosidase
C: Putative 6-phospho-beta-galactobiosidase
D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,49824
Polymers224,8354
Non-polymers2,66320
Water46,4432578
1
D: Putative 6-phospho-beta-galactobiosidase
hetero molecules

A: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,77512
Polymers112,4172
Non-polymers1,35710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
2
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules

C: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,72412
Polymers112,4172
Non-polymers1,30610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
3
A: Putative 6-phospho-beta-galactobiosidase
hetero molecules

D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,77512
Polymers112,4172
Non-polymers1,35710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area6580 Å2
ΔGint-18 kcal/mol
Surface area31640 Å2
MethodPISA
4
C: Putative 6-phospho-beta-galactobiosidase
hetero molecules

B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,72412
Polymers112,4172
Non-polymers1,30610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area6140 Å2
ΔGint-22 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.590, 97.470, 105.270
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative 6-phospho-beta-galactobiosidase


Mass: 56208.730 Da / Num. of mol.: 4 / Mutation: E170Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan1D / Production host: Escherichia coli (E. coli) / References: UniProt: W8QF82, 6-phospho-beta-galactosidase

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 1,5-anhydro-6-O-phosphono-D-glucitol-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 406.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1b_1-5_6*OPO/3O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-0WK / 1,5-anhydro-6-O-phosphono-D-glucitol


Type: D-saccharide / Mass: 244.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O8P
IdentifierTypeProgram
D-1-deoxy-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 2593 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2578 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 398539 / % possible obs: 98.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZE5

4ze5


Resolution: 1.4→22.37 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.741 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 19771 5 %RANDOM
Rwork0.13 ---
obs0.132 373525 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20.04 Å2
2--0.65 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15140 0 173 2578 17891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.01916424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214890
X-RAY DIFFRACTIONr_angle_refined_deg2.671.93522457
X-RAY DIFFRACTIONr_angle_other_deg1.081334250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2552016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84523.528907
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86152581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.45215131
X-RAY DIFFRACTIONr_chiral_restr0.1590.22263
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02119005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024258
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_it1.7261.17575
X-RAY DIFFRACTIONr_mcbond_other1.7181.17572
X-RAY DIFFRACTIONr_mcangle_it2.5721.6469498
X-RAY DIFFRACTIONr_mcangle_other2.5731.6469499
X-RAY DIFFRACTIONr_scbond_it2.9761.3978849
X-RAY DIFFRACTIONr_scbond_other2.9761.3978850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.363212872
X-RAY DIFFRACTIONr_long_range_B_refined7.20211.67722279
X-RAY DIFFRACTIONr_long_range_B_other7.20111.67822280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 1433 -
Rwork0.2 27231 -
obs--97.27 %

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