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- PDB-21ji: Crystal structure of isoprimeverose-producing enzyme from Phaeoac... -

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Basic information

Entry
Database: PDB / ID: 21ji
TitleCrystal structure of isoprimeverose-producing enzyme from Phaeoacremonium minimum
ComponentsIsoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
KeywordsHYDROLASE / Glycoside hydrolase / GH3 / isoprimeverose / xyloglucan
Function / homology
Function and homology information


mating / alpha-glucosidase / alpha-1,4-glucosidase activity / glucan catabolic process / beta-glucosidase / glycogen catabolic process / beta-glucosidase activity / lysosome organization / carbohydrate binding / lysosomal membrane / extracellular region
Similarity search - Function
Mating factor alpha precursor, N-terminal / Mating factor alpha precursor N-terminus / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site ...Mating factor alpha precursor, N-terminal / Mating factor alpha precursor N-terminus / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 31, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Lysosomal alpha-glucosidase / beta-glucosidase
Similarity search - Component
Biological speciesRattus rattus (black rat)
Phaeoacremonium minimum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNakamichi, Y. / Watanabe, M. / Yaoi, K. / Matsuzawa, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01668 Japan
Citation
Journal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural basis for galactose side-chain recognition in isoprimeverose-producing oligoxyloglucan hydrolase from Phaeoacremonium minimum.
Authors: Nakamichi, Y. / Watanabe, M. / Yaoi, K. / Matsuzawa, T.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
B: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
C: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,66659
Polymers283,7213
Non-polymers9,94556
Water84747
1
A: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
hetero molecules

A: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,98348
Polymers189,1472
Non-polymers7,83546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17980 Å2
ΔGint33 kcal/mol
Surface area51610 Å2
MethodPISA
2
B: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
C: Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,17535
Polymers189,1472
Non-polymers6,02833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint14 kcal/mol
Surface area50980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.185, 74.028, 184.494
Angle α, β, γ (deg.)90.000, 95.232, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Isoprimeverose-producing oligoxyloglucan hydrolase,beta-glucosidase / Acid maltase


Mass: 94573.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat), (gene. exp.) Phaeoacremonium minimum (fungus)
Gene: RAG, UCRPA7_4649 / Plasmid: pGAPZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: A0AA49QB00, UniProt: R8BKC2, EC: 3.2.1.120, beta-glucosidase

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Sugars , 3 types, 28 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 22 / Source method: obtained synthetically / 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

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Non-polymers , 6 types, 75 molecules

#5: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Sodium acetate trihydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→49.08 Å / Num. obs: 61469 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 64.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.06 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2615 / CC1/2: 0.674 / Rpim(I) all: 0.476 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
MOLREP11.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.08 Å / SU ML: 0.361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 3073 5 %
Rwork0.2156 58362 -
obs0.2182 61435 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17391 0 642 47 18080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002618420
X-RAY DIFFRACTIONf_angle_d0.569625075
X-RAY DIFFRACTIONf_chiral_restr0.04492912
X-RAY DIFFRACTIONf_plane_restr0.00473213
X-RAY DIFFRACTIONf_dihedral_angle_d14.77637135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.850.341310.31312484X-RAY DIFFRACTION92.14
2.85-2.890.36061360.29792584X-RAY DIFFRACTION99.34
2.89-2.940.34431410.28752678X-RAY DIFFRACTION99.82
2.94-30.35981370.29122603X-RAY DIFFRACTION99.42
3-3.050.34181390.28222663X-RAY DIFFRACTION99.29
3.05-3.120.38081390.2792634X-RAY DIFFRACTION99.36
3.12-3.180.2781380.26442616X-RAY DIFFRACTION99.42
3.18-3.260.32641410.26412671X-RAY DIFFRACTION99.43
3.26-3.340.33891400.25152660X-RAY DIFFRACTION99.4
3.34-3.430.29691380.2372630X-RAY DIFFRACTION99.68
3.43-3.530.28621400.23112659X-RAY DIFFRACTION99.64
3.53-3.640.28451380.21682617X-RAY DIFFRACTION99.53
3.64-3.770.24841410.22152674X-RAY DIFFRACTION99.61
3.77-3.930.28251400.22362666X-RAY DIFFRACTION99.61
3.93-4.10.27221400.20012662X-RAY DIFFRACTION99.57
4.1-4.320.24121410.18722670X-RAY DIFFRACTION99.72
4.32-4.590.26271400.18782663X-RAY DIFFRACTION99.57
4.59-4.950.2381420.18742687X-RAY DIFFRACTION99.54
4.95-5.440.23721400.19482667X-RAY DIFFRACTION99.72
5.44-6.230.24531430.21452709X-RAY DIFFRACTION99.69
6.23-7.840.25991410.20392694X-RAY DIFFRACTION99.37
7.84-49.080.20971470.1772771X-RAY DIFFRACTION98.65

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