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- PDB-7exk: An AA9 LPMO of Ceriporiopsis subvermispora -

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Basic information

Entry
Database: PDB / ID: 7exk
TitleAn AA9 LPMO of Ceriporiopsis subvermispora
ComponentsGlycoside hydrolase family 61 protein
KeywordsOXIDOREDUCTASE / monooxygenase / Auxiliary Activity family 9
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
COPPER (II) ION / alpha-D-xylopyranose / AA9 family lytic polysaccharide monooxygenase
Similarity search - Component
Biological speciesCeriporiopsis subvermispora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsNguyen, H. / Kondo, K. / Nagata, T. / Katahira, M. / Mikami, B.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03192 Japan
Japan Society for the Promotion of Science (JSPS)20K21477 Japan
Japan Society for the Promotion of Science (JSPS)20K06524 Japan
CitationJournal: Acs Sustain Chem Eng / Year: 2022
Title: Functional and Structural Characterizations of Lytic Polysaccharide Monooxygenase, Which Cooperates Synergistically with Cellulases, from Ceriporiopsis subvermispora.
Authors: Nguyen, H. / Kondo, K. / Yagi, Y. / Iseki, Y. / Okuoka, N. / Watanabe, T. / Mikami, B. / Nagata, T. / Katahira, M.
History
DepositionMay 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 61 protein
B: Glycoside hydrolase family 61 protein
C: Glycoside hydrolase family 61 protein
D: Glycoside hydrolase family 61 protein
E: Glycoside hydrolase family 61 protein
F: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,38593
Polymers137,6166
Non-polymers6,76887
Water11,097616
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08615
Polymers22,9361
Non-polymers1,15014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,79525
Polymers22,9361
Non-polymers1,85824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6539
Polymers22,9361
Non-polymers7178
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,88214
Polymers22,9361
Non-polymers94613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,84213
Polymers22,9361
Non-polymers90512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,12817
Polymers22,9361
Non-polymers1,19216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.063, 52.428, 134.625
Angle α, β, γ (deg.)90.000, 90.553, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 26 or resid 28...
d_2ens_1(chain "B" and (resid 1 through 26 or resid 28...
d_3ens_1(chain "C" and (resid 1 through 26 or resid 28...
d_4ens_1(chain "D" and (resid 1 through 26 or resid 28...
d_5ens_1(chain "E" and (resid 1 through 26 or resid 28...
d_6ens_1(chain "F" and (resid 1 through 26 or resid 28...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISHISA1 - 26
d_12ens_1THRASPA30 - 39
d_13ens_1ALASERA41 - 86
d_14ens_1ALAPHEA88 - 113
d_15ens_1ASNTYRA115 - 209
d_16ens_1SERTRPA211 - 217
d_17ens_1GLYGLYA219
d_18ens_1NAGNAGB
d_21ens_1HISHISC1 - 26
d_22ens_1THRASPC28 - 37
d_23ens_1ALASERC41 - 86
d_24ens_1ALAPHEC88 - 113
d_25ens_1ASNTYRC115 - 209
d_26ens_1SERTRPC211 - 217
d_27ens_1GLYGLYC221
d_28ens_1NAGNAGD
d_31ens_1HISHISE1 - 26
d_32ens_1THRASPE28 - 37
d_33ens_1ALASERE39 - 84
d_34ens_1ALAPHEE86 - 111
d_35ens_1ASNTYRE115 - 209
d_36ens_1SERTRPE211 - 217
d_37ens_1GLYGLYE219
d_38ens_1NAGNAGF
d_41ens_1HISHISG1 - 26
d_42ens_1THRASPG28 - 37
d_43ens_1ALASERG39 - 84
d_44ens_1ALAPHEG88 - 113
d_45ens_1ASNTYRG115 - 209
d_46ens_1SERTRPG211 - 217
d_47ens_1GLYGLYG219
d_48ens_1NAGNAGH
d_51ens_1HISHISI1 - 26
d_52ens_1THRASPI30 - 39
d_53ens_1ALASERI43 - 88
d_54ens_1ALAPHEI90 - 115
d_55ens_1ASNTYRI117 - 211
d_56ens_1SERTRPI215 - 221
d_57ens_1GLYGLYI223
d_58ens_1NAGNAGJ
d_61ens_1HISHISK1 - 26
d_62ens_1THRASPK28 - 37
d_63ens_1ALASERK39 - 84
d_64ens_1ALAPHEK86 - 111
d_65ens_1ASNTYRK113 - 207
d_66ens_1SERTRPK209 - 215
d_67ens_1GLYGLYK217
d_68ens_1NAGNAGL

NCS oper:
IDCodeMatrixVector
1given(-0.564652839337, -0.825299265156, -0.00694938570569), (0.825224256675, -0.564427652418, -0.0206482778978), (0.0131185831162, -0.0173939103958, 0.999762649161)22.783743829, -35.7196152282, 44.8651988861
2given(0.528545315556, 0.848904061436, 0.00132056136819), (0.848159481146, -0.528015261939, -0.0427244391617), (-0.0355716733702, 0.0237018488235, -0.99908602153)-21.6865711447, -8.2551840073, 23.5078055424
3given(-0.389612197177, 0.920976488014, 0.00215507236479), (-0.916926154615, -0.388115892811, 0.0928034521412), (0.0863062152635, 0.034181314678, 0.995682115403)39.2572369748, 53.1818546007, 20.5606903992
4given(0.524400826863, -0.851471266402, 0.000674741985584), (-0.851434709212, -0.52438535277, -0.00888469189706), (0.00791888467532, 0.00408464103095, -0.999960302699)41.521212563, 26.1507695676, 44.5238386155
5given(0.999451603598, -0.0321663026588, -0.00786263556516), (0.0324921487199, 0.998431554113, 0.0455926750952), (0.00638375566062, -0.0458231461604, 0.998929170132)-0.578708703444, -1.75890105826, 67.3701275812

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glycoside hydrolase family 61 protein


Mass: 22936.076 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceriporiopsis subvermispora (strain B) (fungus)
Gene: CERSUDRAFT_85414 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: M2RAI8

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Sugars , 2 types, 7 molecules

#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.: 6 / 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
#6: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 696 molecules

#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.16 Å3/Da / Density % sol: 43.13 % / Description: rectangle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.78 mg/mL protein with equal volume of 0.1 M CaCl2, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→48.9 Å / Num. obs: 61984 / % possible obs: 95.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.073 / Net I/σ(I): 15.46
Reflection shellResolution: 2.14→2.27 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.49 / Num. unique obs: 7982 / CC1/2: 0.933 / Rrim(I) all: 0.284 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5Q

4b5q


Resolution: 2.14→48.85 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.0288
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 3100 5 %
Rwork0.1723 58863 -
obs0.1752 61963 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.17 Å2
Refinement stepCycle: LAST / Resolution: 2.14→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 413 616 10779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710465
X-RAY DIFFRACTIONf_angle_d0.909914278
X-RAY DIFFRACTIONf_chiral_restr0.0571535
X-RAY DIFFRACTIONf_plane_restr0.00671882
X-RAY DIFFRACTIONf_dihedral_angle_d15.93073569
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.475775087556
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.434112389669
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.417736004817
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.511389553683
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.453103313593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.180.30371010.20681906X-RAY DIFFRACTION68.38
2.18-2.210.28521090.19632070X-RAY DIFFRACTION74.83
2.21-2.250.26571190.19942272X-RAY DIFFRACTION81.3
2.25-2.290.26521270.19652415X-RAY DIFFRACTION87
2.29-2.340.25321350.19752567X-RAY DIFFRACTION93.14
2.34-2.390.25471460.19542757X-RAY DIFFRACTION98.81
2.39-2.440.26661450.19852770X-RAY DIFFRACTION100
2.44-2.490.26311480.19382806X-RAY DIFFRACTION99.9
2.49-2.560.25071450.19522756X-RAY DIFFRACTION99.79
2.56-2.630.2721490.19152828X-RAY DIFFRACTION99.8
2.63-2.70.26871450.19462745X-RAY DIFFRACTION99.9
2.7-2.790.27611460.19762777X-RAY DIFFRACTION99.86
2.79-2.890.28721480.19132813X-RAY DIFFRACTION99.8
2.89-30.24691460.17992779X-RAY DIFFRACTION99.73
3-3.140.21781470.17912783X-RAY DIFFRACTION99.86
3.14-3.310.24211470.17442803X-RAY DIFFRACTION100
3.31-3.510.21891480.16272814X-RAY DIFFRACTION99.76
3.51-3.790.20241480.15662803X-RAY DIFFRACTION99.86
3.79-4.170.16851470.14392808X-RAY DIFFRACTION99.93
4.17-4.770.19411500.13662842X-RAY DIFFRACTION99.8
4.77-60.2181490.14982835X-RAY DIFFRACTION99.8
6.01-48.850.21391550.18912914X-RAY DIFFRACTION98.62

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