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- PDB-5zhb: Structure of Cellobiose 2-Epimerase from Bacillus thermoamylovora... -

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Basic information

Entry
Database: PDB / ID: 5zhb
TitleStructure of Cellobiose 2-Epimerase from Bacillus thermoamylovorans B4167
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / cellobiose 2-epimerase / epimerization / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


cellobiose epimerase / cellobiose epimerase activity / carbohydrate metabolic process
Similarity search - Function
Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Cellobiose 2-epimerase
Similarity search - Component
Biological speciesCaldibacillus thermoamylovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFeng, Y.H. / Yang, R.J. / Andrew, J.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Cellobiose 2-Epimerase from Bacillus thermoamylovorans B4167
Authors: Feng, Y.H. / Yang, R.J. / Andrew, J.F.
History
DepositionMar 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn / entity / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.angle_beta / _chem_comp.formula ..._cell.angle_beta / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal_grow.pdbx_details / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _software.name / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellobiose 2-epimerase
B: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)92,6342
Polymers92,6342
Non-polymers00
Water3,837213
1
A: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)46,3171
Polymers46,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose 2-epimerase


Theoretical massNumber of molelcules
Total (without water)46,3171
Polymers46,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.979, 52.336, 129.602
Angle α, β, γ (deg.)90.000, 129.945, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellobiose 2-epimerase / CE


Mass: 46316.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldibacillus thermoamylovorans (bacteria)
Gene: B4166_1736, B4167_1620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D0GHZ5, cellobiose epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Trimethylamine-N-oxide, 0.1M Tris-HCl, pH8.5,20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 83031 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.05 / Net I/σ(I): 15.72
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 5958 / CC1/2: 0.794 / Rrim(I) all: 0.729 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.181 / SU B: 3.886 / SU ML: 0.112 / Average fsc free: 0.9536 / Average fsc work: 0.9666 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 3916 5.107 %RANDOM
Rwork0.1964 72768 --
all0.199 ---
obs-76684 98.147 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.056 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å2-0 Å20.006 Å2
2---0.044 Å2-0 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 0 213 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126811
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166120
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.8319235
X-RAY DIFFRACTIONr_angle_other_deg0.6021.78714067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.923533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.971101160
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.01310389
X-RAY DIFFRACTIONr_chiral_restr0.0920.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021739
X-RAY DIFFRACTIONr_nbd_refined0.230.21474
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.25702
X-RAY DIFFRACTIONr_nbtor_refined0.1920.23317
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.28
X-RAY DIFFRACTIONr_nbd_other0.2190.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.28
X-RAY DIFFRACTIONr_mcbond_it2.9283.2223158
X-RAY DIFFRACTIONr_mcbond_other2.9283.2213157
X-RAY DIFFRACTIONr_mcangle_it4.2145.7753962
X-RAY DIFFRACTIONr_mcangle_other4.2145.7763963
X-RAY DIFFRACTIONr_scbond_it3.5413.523653
X-RAY DIFFRACTIONr_scbond_other3.5413.523654
X-RAY DIFFRACTIONr_scangle_it5.5556.3055272
X-RAY DIFFRACTIONr_scangle_other5.5546.3055273
X-RAY DIFFRACTIONr_lrange_it8.36231.0347985
X-RAY DIFFRACTIONr_lrange_other8.26730.897960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.3372900.32153480.32256960.9190.92298.98170.276
1.898-1.950.3353090.29452370.29656050.9180.93898.94740.252
1.95-2.0060.3072870.26750890.26954520.9390.9598.6060.227
2.006-2.0680.2822390.25149380.25352410.9420.95898.77890.213
2.068-2.1350.272480.22947410.23151190.9560.96797.46040.197
2.135-2.210.2672330.22244480.22549510.950.96894.54660.191
2.21-2.2930.2592700.21444880.21747960.9610.97299.20770.186
2.293-2.3870.2682410.20743450.21146220.9570.97499.22110.18
2.387-2.4920.2162260.18641720.18844440.9710.97998.96490.16
2.492-2.6130.2442030.18439600.18742120.9670.97998.83670.164
2.613-2.7540.2672000.19237700.19640360.9580.97898.36470.172
2.754-2.920.2451790.19734720.19938010.9590.97696.05370.179
2.92-3.1210.2711880.19533560.19935810.9570.97798.96680.182
3.121-3.3690.241770.19831230.20133380.9640.97598.86160.189
3.369-3.6880.231640.19829100.231260.9680.97898.33650.193
3.688-4.1190.1951280.16925690.17127960.9770.98496.45920.172
4.119-4.7470.1931110.14523540.14725130.9810.98898.08990.151
4.747-5.7940.2111140.1719860.17221270.9790.98698.73060.176
5.794-8.1070.21750.18315200.18416650.9780.98395.79580.189
8.107-39.630.128340.1619420.169980.9910.98597.79560.181

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