[English] 日本語
Yorodumi
- PDB-8idp: Crystal structure of reducing-end xylose-releasing exoxylanase in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8idp
TitleCrystal structure of reducing-end xylose-releasing exoxylanase in GH30 from Talaromyces cellulolyticus
ComponentsReducing-end xylose-releasing exoxylanase Xyn30A
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Reducing-end xylose-releasing exoxylanase Xyn30A
Similarity search - Component
Biological speciesTalaromyces pinophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamichi, Y. / Watanabe, M. / Fujii, T. / Inoue, H. / Morita, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of reducing-end xylose-releasing exoxylanase in subfamily 7 of glycoside hydrolase family 30.
Authors: Nakamichi, Y. / Watanabe, M. / Fujii, T. / Inoue, H. / Morita, T.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reducing-end xylose-releasing exoxylanase Xyn30A
C: Reducing-end xylose-releasing exoxylanase Xyn30A
B: Reducing-end xylose-releasing exoxylanase Xyn30A
D: Reducing-end xylose-releasing exoxylanase Xyn30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,47642
Polymers204,3064
Non-polymers16,17038
Water27,4011521
1
A: Reducing-end xylose-releasing exoxylanase Xyn30A
C: Reducing-end xylose-releasing exoxylanase Xyn30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,31022
Polymers102,1532
Non-polymers8,15720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17600 Å2
ΔGint157 kcal/mol
Surface area30700 Å2
MethodPISA
2
B: Reducing-end xylose-releasing exoxylanase Xyn30A
D: Reducing-end xylose-releasing exoxylanase Xyn30A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,16620
Polymers102,1532
Non-polymers8,01318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17200 Å2
ΔGint159 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.457, 120.072, 122.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2512-

HOH

-
Components

-
Protein , 1 types, 4 molecules ACBD

#1: Protein
Reducing-end xylose-releasing exoxylanase Xyn30A


Mass: 51076.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces pinophilus (fungus) / Gene: TCE0_047r17950 / Production host: Talaromyces pinophilus (fungus) / References: UniProt: A0A0B8MZ29

-
Sugars , 7 types, 19 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-h1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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

-
Non-polymers , 4 types, 1540 molecules

#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1521 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, 0.1 M Tris-HCl, 0.2 M lithium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→45.96 Å / Num. obs: 188427 / % possible obs: 97.9 % / Redundancy: 5 % / CC1/2: 0.994 / Rpim(I) all: 0.05 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 97250 / CC1/2: 0.82 / Rpim(I) all: 0.257

-
Processing

Software
NameVersionClassification
XDSMar 15, 2019data scaling
XDSMar 15, 2019data reduction
MOLREP11.6phasing
PHENIX1.12refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.94 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 9420 5 %0
Rwork0.1651 ---
obs0.1666 188371 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13933 0 1076 1521 16530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.894
X-RAY DIFFRACTIONf_dihedral_angle_d7.9252664
X-RAY DIFFRACTIONf_chiral_restr0.0552465
X-RAY DIFFRACTIONf_plane_restr0.0072643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.25543020.21835741X-RAY DIFFRACTION96
1.82-1.840.24813110.20975896X-RAY DIFFRACTION100
1.84-1.860.23623120.19325932X-RAY DIFFRACTION100
1.86-1.890.24063140.18255963X-RAY DIFFRACTION100
1.89-1.910.20793120.1825934X-RAY DIFFRACTION100
1.91-1.940.22673130.17865937X-RAY DIFFRACTION100
1.94-1.970.2133110.17715922X-RAY DIFFRACTION100
1.97-20.22583130.1735940X-RAY DIFFRACTION100
2-2.030.2023120.16855924X-RAY DIFFRACTION100
2.03-2.060.20343130.15915949X-RAY DIFFRACTION100
2.06-2.10.18993110.16525922X-RAY DIFFRACTION100
2.1-2.130.22843140.16985959X-RAY DIFFRACTION100
2.13-2.170.1963140.16065972X-RAY DIFFRACTION100
2.17-2.220.20173120.15775923X-RAY DIFFRACTION100
2.22-2.270.1933140.15415970X-RAY DIFFRACTION100
2.27-2.320.19613150.15635983X-RAY DIFFRACTION100
2.32-2.380.19163120.15535930X-RAY DIFFRACTION100
2.38-2.440.18413140.15955956X-RAY DIFFRACTION100
2.44-2.510.21343140.16395968X-RAY DIFFRACTION100
2.51-2.60.2023130.15965945X-RAY DIFFRACTION100
2.6-2.690.19253150.15945986X-RAY DIFFRACTION100
2.69-2.80.21493140.16535968X-RAY DIFFRACTION100
2.8-2.920.19423130.16275942X-RAY DIFFRACTION99
2.92-3.080.20213160.16356001X-RAY DIFFRACTION99
3.08-3.270.19433130.16385960X-RAY DIFFRACTION99
3.27-3.520.1773190.1616044X-RAY DIFFRACTION99
3.52-3.880.15933160.1486018X-RAY DIFFRACTION99
3.88-4.440.16833170.14896019X-RAY DIFFRACTION99
4.44-5.590.18043200.15856075X-RAY DIFFRACTION99
5.59-40.940.21073310.20266272X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9906-0.85570.11021.6221-0.28371.1527-0.0090.05630.1157-0.0806-0.0036-0.1471-0.05820.00650.00160.0209-0.04410.00720.11970.01350.148767.893228.203250.4031
21.3558-0.49510.62080.7088-0.29090.87-0.0040.10160.1571-0.0068-0.0359-0.1359-0.0690.06550.03710.1284-0.0150.01490.1280.01880.123152.082943.234941.8659
30.7266-0.6865-0.35921.2860.13641.0676-0.00710.00050.0747-0.02210.0073-0.063-0.05910.063-0.00350.0971-0.0219-0.01360.11490.02040.124266.107828.972552.229
41.53080.50750.87962.5695-0.79072.777-0.02830.2713-0.0668-0.3174-0.0314-0.42070.1310.50740.07080.13670.0190.03470.21680.02350.218679.080118.835847.7981
50.39270.09460.3650.49910.34171.1041-0.02310.0561-0.0341-0.07280.0257-0.10760.06040.18750.00190.14950.02220.03810.1855-0.01010.18134.471520.146-3.7751
63.26811.3931.76450.96660.87822.5649-0.13040.7809-0.3404-0.22340.2038-0.15280.02620.2506-0.0910.2508-0.00610.07460.2353-0.06090.198121.75112.5117-25.9114
71.24080.6057-0.02220.9565-0.13310.5008-0.03320.0824-0.1687-0.09370.0258-0.0420.06420.01770.00730.14620.00310.02860.1391-0.02450.10914.630510.3614-10.291
80.3912-0.07940.51320.9899-0.03790.7766-0.00930.0192-0.0065-0.06660.0087-0.07660.06260.06650.00490.12890.00870.03810.1454-0.01180.122331.475522.23311.7356
91.750.8274-0.42312.18961.01622.5541-0.0507-0.1108-0.3680.1120.0585-0.50640.3580.417-0.01230.1570.0620.00620.22980.00470.229344.310218.011611.8855
101.21840.86310.29991.93190.94881.2814-0.0508-0.05630.1869-0.0935-0.0480.3255-0.1606-0.16720.08410.09950.02190.00680.1847-0.01620.1455-1.486134.014211.1613
111.03260.49590.57420.74650.46640.8382-0.0417-0.05340.07260.0114-0.03010.0621-0.0563-0.04370.07210.12640.01180.01210.1324-0.00010.105613.829840.277916.8939
121.3194-0.31520.88582.02770.81481.4855-0.0263-0.2571-0.11110.2409-0.05740.40130.1446-0.37760.06880.1362-0.03830.05660.2192-0.0150.1985-8.663818.171913.6375
130.5607-0.19220.40010.978-0.68281.20470.0014-0.0749-0.07690.03980.08690.12240.058-0.2136-0.07390.0837-0.02160.00470.16430.02020.142233.555518.474664.9344
144.2501-2.63162.55641.6844-1.44892.5284-0.1576-0.4923-0.11870.15810.26960.0922-0.2207-0.2534-0.11250.16880.00460.02860.1690.02150.143646.679610.650785.8482
151.1858-0.68340.17890.9909-0.26190.63730.00620.0012-0.0548-0.0367-0.0035-0.01440.0402-0.03520.00080.1122-0.0177-0.00050.12520.00290.101253.93159.636870.0777
160.62120.0550.47051.06620.08571.32340.01110.0136-0.0064-0.01750.04190.0589-0.0127-0.0279-0.04950.1059-0.00090.00430.14270.02540.117236.321421.237559.0381
171.7174-0.8846-0.02561.4753-1.32853.0528-0.04860.1119-0.3823-0.33720.1280.38920.4234-0.3372-0.07230.1684-0.0649-0.0340.21360.01540.212225.499614.838747.3039
181.3405-1.0762-1.11191.6828-0.22232.4627-0.03550.0516-0.1932-0.1883-0.00240.58090.2425-0.45230.04740.1433-0.0405-0.04590.25140.05370.229921.689819.423549.7147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 17 through 60 )
2X-RAY DIFFRACTION2chain 'D' and (resid 61 through 300 )
3X-RAY DIFFRACTION3chain 'D' and (resid 301 through 390 )
4X-RAY DIFFRACTION4chain 'D' and (resid 391 through 462 )
5X-RAY DIFFRACTION5chain 'A' and (resid 17 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 300 )
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 390 )
9X-RAY DIFFRACTION9chain 'A' and (resid 391 through 462 )
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 86 )
11X-RAY DIFFRACTION11chain 'C' and (resid 87 through 365 )
12X-RAY DIFFRACTION12chain 'C' and (resid 366 through 462 )
13X-RAY DIFFRACTION13chain 'B' and (resid 17 through 86 )
14X-RAY DIFFRACTION14chain 'B' and (resid 87 through 127 )
15X-RAY DIFFRACTION15chain 'B' and (resid 128 through 300 )
16X-RAY DIFFRACTION16chain 'B' and (resid 301 through 390 )
17X-RAY DIFFRACTION17chain 'B' and (resid 391 through 428 )
18X-RAY DIFFRACTION18chain 'B' and (resid 429 through 462 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more