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- PDB-1fmi: CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE -

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Basic information

Entry
Database: PDB / ID: 1fmi
TitleCRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE
ComponentsENDOPLASMIC RETICULUM ALPHA-MANNOSIDASE I
KeywordsHYDROLASE / alpha-alpha7 barrel
Function / homology
Function and homology information


trimming of terminal mannose on C branch / endoplasmic reticulum N-glycan trimming / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / oligosaccharide metabolic process / endoplasmic reticulum quality control compartment / ERAD pathway / ER Quality Control Compartment (ERQC) ...trimming of terminal mannose on C branch / endoplasmic reticulum N-glycan trimming / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / oligosaccharide metabolic process / endoplasmic reticulum quality control compartment / ERAD pathway / ER Quality Control Compartment (ERQC) / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / 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
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsVallee, F. / Karaveg, K. / Herscovics, A. / Moremen, K.W. / Howell, P.L.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural basis for catalysis and inhibition of N-glycan processing class I alpha 1,2-mannosidases.
Authors: Vallee, F. / Karaveg, K. / Herscovics, A. / Moremen, K.W. / Howell, P.L.
History
DepositionAug 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_ins_code / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOPLASMIC RETICULUM ALPHA-MANNOSIDASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9125
Polymers52,5841
Non-polymers3284
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.829, 95.829, 136.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein ENDOPLASMIC RETICULUM ALPHA-MANNOSIDASE I / CLASS I ALPHA1 / 2-MANNOSIDASE


Mass: 52583.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPROTA-ERMANI / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q9UKM7, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MES, NaCl, CaCl2, Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMES1drop
3150 mM1dropNaCl
45 mM1dropCaCl2
50.25 MNDSB2011drop
61.6-1.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.05
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 226830 / Num. obs: 226830 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.46 / Num. unique all: 55846 / % possible all: 97.3
Reflection
*PLUS
Num. obs: 55846 / Num. measured all: 226830
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4Brefinement
RefinementResolution: 1.9→28.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 329247.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2738 5.1 %RANDOM
Rwork0.222 ---
all0.222 226830 --
obs0.222 54056 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.49 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å22.92 Å20 Å2
2--4.61 Å20 Å2
3----9.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 16 391 4089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.512
X-RAY DIFFRACTIONc_scbond_it1.42
X-RAY DIFFRACTIONc_scangle_it2.122.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 470 5.6 %
Rwork0.299 7966 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.4B / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.299

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