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- PDB-2xsg: Structure of the gh92 family glycosyl hydrolase ccman5 -

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Basic information

Entry
Database: PDB / ID: 2xsg
TitleStructure of the gh92 family glycosyl hydrolase ccman5
ComponentsCCMAN5
KeywordsHYDROLASE / MANNOSIDASE
Function / homologyBeta-galactosidase; Chain A, domain 5 - #10 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta
Function and homology information
Biological speciesCELLULOSIMICROBIUM CELLULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBaranova, E. / Tiels, P. / Remaut, H.
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: A Bacterial Glycosidase Enables Mannose-6-Phosphate Modification and Improved Cellular Uptake of Yeast-Produced Recombinant Human Lysosomal Enzymes.
Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / ...Authors: Tiels, P. / Baranova, E. / Piens, K. / De Visscher, C. / Pynaert, G. / Nerinckx, W. / Stout, J. / Fudalej, F. / Hulpiau, P. / Tannler, S. / Geysens, S. / Van Hecke, A. / Valevska, A. / Vervecken, W. / Remaut, H. / Callewaert, N.
History
DepositionSep 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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

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Assembly

Deposited unit
A: CCMAN5
B: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5576
Polymers165,1022
Non-polymers4554
Water15,637868
1
A: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8733
Polymers82,5511
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CCMAN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6833
Polymers82,5511
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.202, 91.158, 224.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-2037-

HOH

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Components

#1: Protein CCMAN5


Mass: 82551.070 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-774
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLULOSIMICROBIUM CELLULANS (bacteria)
Description: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMS, STRAIN NUMBER LMG 16121
Plasmid: PLSAHCCMAN5DOMAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: alpha-mannosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Description: PHASES WERE DETERMINED ON KAUCL4 SOAKED CRYSTAL. DEPOSITED STRUCTURE FACTORS AND COORDINATES ARE FROM NATIVE CRYSTAL.
Crystal growpH: 7.5
Details: 0.2 M NAF, 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→47.8 Å / Num. obs: 106820 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→47.8 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.867 / SU B: 4.025 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23861 5629 5 %RANDOM
Rwork0.19067 ---
obs0.19303 106820 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11513 0 19 868 12400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.93516128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94951527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57623.891550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.541151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5121572
X-RAY DIFFRACTIONr_chiral_restr0.0840.21746
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219368
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_it0.4851.57541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.872212017
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.60534275
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5394.54111
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: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 357 -
Rwork0.244 6689 -
obs--83.47 %

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