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- PDB-4lyp: Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase fro... -

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Basic information

Entry
Database: PDB / ID: 4lyp
TitleCrystal Structure of Glycoside Hydrolase Family 5 Mannosidase from Rhizomucor miehei
ComponentsExo-beta-1,4-mannosidase
KeywordsHYDROLASE / Tim Barrel / extracellular protein
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / GUANIDINE
Function and homology information
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsJiang, Z.Q. / Zhou, P. / Yang, S.Q. / Liu, Y. / Yan, Q.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 beta-mannosidase.
Authors: Zhou, P. / Liu, Y. / Yan, Q. / Chen, Z. / Qin, Z. / Jiang, Z.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Oct 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: Exo-beta-1,4-mannosidase
B: Exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0768
Polymers102,5962
Non-polymers4816
Water23,1131283
1
A: Exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5384
Polymers51,2981
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5384
Polymers51,2981
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.646, 171.991, 55.137
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exo-beta-1,4-mannosidase


Mass: 51297.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Production host: Escherichia coli (E. coli) / References: beta-mannosidase
#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% PEG 4000, 0.2 M guanidine hydrochloride, 0.1M HEPES buffer pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.28→86 Å / Num. all: 235043 / Num. obs: 205153 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.052
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.28-1.3191.4
3.47-20127.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.983 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15344 10147 5 %RANDOM
Rwork0.11932 ---
all0.12102 ---
obs0.12102 192973 86.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.06 Å2
2---0.59 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 32 1283 8015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.027105
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9359681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69424.348368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.308151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0921536
X-RAY DIFFRACTIONr_chiral_restr0.1280.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215682
X-RAY DIFFRACTIONr_rigid_bond_restr7.47937105
X-RAY DIFFRACTIONr_sphericity_free34.9645288
X-RAY DIFFRACTIONr_sphericity_bonded11.33957869
LS refinement shellResolution: 1.277→1.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 747 -
Rwork0.372 13556 -
obs--82.63 %

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