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- PDB-8b48: Structure of Lentithecium fluviatile carbohydrate esterase from t... -

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Basic information

Entry
Database: PDB / ID: 8b48
TitleStructure of Lentithecium fluviatile carbohydrate esterase from the CE15 family (LfCE15C)
ComponentsCarbohydrate esterase family 15 protein
KeywordsHYDROLASE / Lignocellulose degradation
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold / FORMIC ACID / Carbohydrate esterase family 15 protein
Function and homology information
Biological speciesLentithecium fluviatile (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsScholzen, K. / Mazurkewich, S. / Poulsen, J.C.N. / Larsbrink, J. / Lo Leggio, L.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0027698 Denmark
Novo Nordisk FoundationNNF21OC0071611 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and functional investigation of a fungal member of carbohydrate esterase family 15 with potential specificity for rare xylans.
Authors: Mazurkewich, S. / Scholzen, K.C. / Brusch, R.H. / Poulsen, J.C.N. / Theibich, Y. / Huttner, S. / Olsson, L. / Larsbrink, J. / Lo Leggio, L.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate esterase family 15 protein
B: Carbohydrate esterase family 15 protein
C: Carbohydrate esterase family 15 protein
D: Carbohydrate esterase family 15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,63810
Polymers172,9024
Non-polymers3,7356
Water5,459303
1
A: Carbohydrate esterase family 15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0203
Polymers43,2261
Non-polymers7952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbohydrate esterase family 15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1362
Polymers43,2261
Non-polymers9111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbohydrate esterase family 15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2992
Polymers43,2261
Non-polymers1,0731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbohydrate esterase family 15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1823
Polymers43,2261
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.740, 79.570, 86.010
Angle α, β, γ (deg.)113.322, 98.531, 94.440
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEUAA20 - 3894 - 373
221SERSERLEULEUBB20 - 3894 - 373
332SERSERLEULEUAA20 - 3894 - 373
442SERSERLEULEUCC20 - 3894 - 373
553CYSCYSGLYGLYAA21 - 3885 - 372
663CYSCYSGLYGLYDD21 - 3885 - 372
774SERSERLEULEUBB20 - 3894 - 373
884SERSERLEULEUCC20 - 3894 - 373
995CYSCYSGLYGLYBB21 - 3885 - 372
10105CYSCYSGLYGLYDD21 - 3885 - 372
11116CYSCYSGLYGLYCC21 - 3885 - 372
12126CYSCYSGLYGLYDD21 - 3885 - 372

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbohydrate esterase family 15 protein


Mass: 43225.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentithecium fluviatile (fungus) / Gene: K458DRAFT_349146 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: A0A6G1IIU9

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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
#4: 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.: 1
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

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Non-polymers , 2 types, 305 molecules

#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock: 13.7 mg/mL in 20 mM Tris pH 8.0 Reservoir: 0.2 M Ammonium formate pH 6.6, 20 %w/v PEG 3350 Drop: 3:1 protein to reservoir ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.980779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980779 Å / Relative weight: 1
ReflectionResolution: 2.65→47.254 Å / Num. obs: 47781 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.982 / Net I/σ(I): 4.3
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3530 / CC1/2: 0.513 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIC

3pic


Resolution: 2.65→47.254 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / SU B: 29.729 / SU ML: 0.509 / Cross valid method: FREE R-VALUE / ESU R Free: 0.415
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2977 2294 4.801 %
Rwork0.2379 45487 -
all0.241 --
obs-47781 97.626 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.101 Å2
Baniso -1Baniso -2Baniso -3
1-4.938 Å2-2.676 Å25.124 Å2
2---2.868 Å2-2.909 Å2
3----0.623 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11382 0 250 303 11935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312005
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711023
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.67416324
X-RAY DIFFRACTIONr_angle_other_deg1.1831.60425502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22551485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50922.208566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73151844
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg13.788152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0851564
X-RAY DIFFRACTIONr_chiral_restr0.0570.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022738
X-RAY DIFFRACTIONr_nbd_refined0.1990.22371
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.210583
X-RAY DIFFRACTIONr_nbtor_refined0.1640.25701
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.25665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2338
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.228
X-RAY DIFFRACTIONr_nbd_other0.280.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.210
X-RAY DIFFRACTIONr_mcbond_it4.4196.1555922
X-RAY DIFFRACTIONr_mcbond_other4.4186.1555923
X-RAY DIFFRACTIONr_mcangle_it6.8599.2247398
X-RAY DIFFRACTIONr_mcangle_other6.8589.2267399
X-RAY DIFFRACTIONr_scbond_it4.5836.5656083
X-RAY DIFFRACTIONr_scbond_other4.5836.5656079
X-RAY DIFFRACTIONr_scangle_it7.0429.7028921
X-RAY DIFFRACTIONr_scangle_other7.0419.7028922
X-RAY DIFFRACTIONr_lrange_it11.823117.41950523
X-RAY DIFFRACTIONr_lrange_other11.821117.47650444
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.0512100
X-RAY DIFFRACTIONr_ncsr_local_group_20.060.0512150
X-RAY DIFFRACTIONr_ncsr_local_group_30.0550.0512143
X-RAY DIFFRACTIONr_ncsr_local_group_40.0640.0512166
X-RAY DIFFRACTIONr_ncsr_local_group_50.0660.0512104
X-RAY DIFFRACTIONr_ncsr_local_group_60.0460.0512136
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.070150.0501
12BX-RAY DIFFRACTIONLocal ncs0.070150.0501
23AX-RAY DIFFRACTIONLocal ncs0.060310.0501
24CX-RAY DIFFRACTIONLocal ncs0.060310.0501
35AX-RAY DIFFRACTIONLocal ncs0.055430.0501
36DX-RAY DIFFRACTIONLocal ncs0.055430.0501
47BX-RAY DIFFRACTIONLocal ncs0.064250.0501
48CX-RAY DIFFRACTIONLocal ncs0.064250.0501
59BX-RAY DIFFRACTIONLocal ncs0.066010.0501
510DX-RAY DIFFRACTIONLocal ncs0.066010.0501
611CX-RAY DIFFRACTIONLocal ncs0.046140.0501
612DX-RAY DIFFRACTIONLocal ncs0.046140.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.7190.4841820.4553350X-RAY DIFFRACTION97.3271
2.719-2.7930.4591900.413256X-RAY DIFFRACTION98.1487
2.793-2.8740.3841400.43227X-RAY DIFFRACTION97.6791
2.874-2.9620.3831440.3663135X-RAY DIFFRACTION98.1737
2.962-3.0590.4231550.3323022X-RAY DIFFRACTION97.8442
3.059-3.1670.3761510.3032876X-RAY DIFFRACTION97.8978
3.167-3.2860.3691550.2862779X-RAY DIFFRACTION97.8652
3.286-3.420.3491340.2762710X-RAY DIFFRACTION97.6648
3.42-3.5720.3471350.262570X-RAY DIFFRACTION97.1275
3.572-3.7460.3461300.2522457X-RAY DIFFRACTION96.8914
3.746-3.9480.2461090.2192369X-RAY DIFFRACTION97.1765
3.948-4.1860.236990.192169X-RAY DIFFRACTION96.5928
4.186-4.4750.271090.1732072X-RAY DIFFRACTION97.0196
4.475-4.8320.2031040.1721931X-RAY DIFFRACTION97.7426
4.832-5.2910.211790.1521807X-RAY DIFFRACTION97.619
5.291-5.9120.205720.1681634X-RAY DIFFRACTION98.442
5.912-6.820.208640.161443X-RAY DIFFRACTION98.0481
6.82-8.3360.203770.1451211X-RAY DIFFRACTION98.6217
8.336-11.7220.167450.157956X-RAY DIFFRACTION98.8154
11.722-47.2540.448200.27513X-RAY DIFFRACTION94.8399

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