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- PDB-1hcu: alpha-1,2-mannosidase from Trichoderma reesei -

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Basic information

Entry
Database: PDB / ID: 1hcu
Titlealpha-1,2-mannosidase from Trichoderma reesei
ComponentsALPHA-1,2-MANNOSIDASE
KeywordsGLYCOSYLATION / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / : / ERAD pathway / carbohydrate metabolic process / calcium ion binding / endoplasmic reticulum / membrane
Similarity search - Function
: / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
alpha-1,2-Mannosidase
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsVan Petegem, F. / Contreras, H. / Contreras, R. / Van Beeumen, J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Trichoderma Reesei Alpha-1,2-Mannosidase: Structural Basis for the Cleavage of Four Consecutive Mannose Residues
Authors: Van Petegem, F. / Contreras, H. / Contreras, R. / Van Beeumen, J.
History
DepositionMay 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 13, 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
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,2-MANNOSIDASE
B: ALPHA-1,2-MANNOSIDASE
C: ALPHA-1,2-MANNOSIDASE
D: ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,81118
Polymers217,4384
Non-polymers2,37214
Water19,7081094
1
A: ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0635
Polymers54,3601
Non-polymers7044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0635
Polymers54,3601
Non-polymers7044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8424
Polymers54,3601
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8424
Polymers54,3601
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.201, 106.836, 101.388
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.97622, 0.21303, 0.04015), (-0.21542, 0.93256, 0.28971), (0.02427, -0.29147, 0.95627)-8.98176, 61.13692, 43.2628
2given(-0.97617, -0.21358, -0.03833), (0.21676, -0.96789, -0.12728), (-0.00992, -0.13255, 0.99113)43.84169, 57.47837, 43.67975
3given(0.99993, 0.00556, 0.01061), (0.00677, -0.99298, -0.1181), (0.00987, 0.11816, -0.99295)18.78967, 58.71406, 99.9332

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Components

#1: Protein
ALPHA-1,2-MANNOSIDASE / 1 / 2-A-D-MANNOSIDASE


Mass: 54359.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: PICHIA PASTORIS (fungus)
References: UniProt: Q9P8T8, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.102 Å3/Da / Density % sol: 39.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: 10MG/ML PROTEIN IN 0.1M TRIS-CL PH 7.5 MIX 2 MICROLITER OF PROTEIN SOLUTION WITH 2 MICROLITER OF WELL SOLUTION IN A HANGING DROP EXPERIMENT. THE WELL CONTAINS 0.1M NA-ACETATE PH 4.0, 12% PEG 35000, 0.3M CACL2
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
325 mM1dropNaCl
40.1 Msodium acetate1reservoir
50.3 M1reservoirCaCl2
612.5 %(w/v)PEG350001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.37→20 Å / Num. obs: 73996 / % possible obs: 98.9 % / Redundancy: 4.94 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.01
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 4.915 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 818429
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DL2

1dl2


Resolution: 2.37→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 3683 5 %RANDOM
Rwork0.1772 ---
obs0.1772 73042 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.35 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å2-5.79 Å2
2--0.71 Å20 Å2
3---3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14846 0 144 1094 16084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1641.5
X-RAY DIFFRACTIONc_mcangle_it1.9562
X-RAY DIFFRACTIONc_scbond_it1.7962
X-RAY DIFFRACTIONc_scangle_it2.6812.5
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 565 4.8 %
Rwork0.204 11242 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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