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- PDB-3eja: Magnesium-bound glycoside hydrolase 61 isoform E from Thielavia t... -

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Basic information

Entry
Database: PDB / ID: 3eja
TitleMagnesium-bound glycoside hydrolase 61 isoform E from Thielavia terrestris
Componentsprotein GH61E
KeywordsUNKNOWN FUNCTION / beta sandwich / fibronectin type III fold / metal site / magnesium
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesThielavia terrestris (fungus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.902 Å
AuthorsSalbo, R. / Welner, D. / Lo Leggio, L. / Harris, P. / McFarland, K.
CitationJournal: Biochemistry / Year: 2010
Title: Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family.
Authors: Harris, P.V. / Welner, D. / McFarland, K.C. / Re, E. / Navarro Poulsen, J.C. / Brown, K. / Salbo, R. / Ding, H. / Vlasenko, E. / Merino, S. / Xu, F. / Cherry, J. / Larsen, S. / Lo Leggio, L.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein GH61E
B: protein GH61E
C: protein GH61E
D: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,50325
Polymers90,2804
Non-polymers2,22321
Water15,331851
1
A: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1967
Polymers22,5701
Non-polymers6266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1046
Polymers22,5701
Non-polymers5345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0085
Polymers22,5701
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1967
Polymers22,5701
Non-polymers6266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)221.461, 221.461, 221.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A19
2113B19
3113C19
4113D19
1211A20
2211B20
3211C20
4211D20
1313A21
2313B21
3313C21
4313D21
1411A22
2411B22
3411C22
4411D22
1513A23 - 24
2513B23 - 24
3513C23 - 24
4513D23 - 24
1611A25
2611B25
3611C25
4611D25
1713A26 - 27
2713B26 - 27
3713C26 - 27
4713D26 - 27
1811A28 - 31
2811B28 - 31
3811C28 - 31
4811D28 - 31
1913A32 - 33
2913B32 - 33
3913C32 - 33
4913D32 - 33
11011A34
21011B34
31011C34
41011D34
11116A35 - 36
21116B35 - 36
31116C35 - 36
41116D35 - 36
11211A37 - 39
21211B37 - 39
31211C37 - 39
41211D37 - 39
11316A40 - 43
21316B40 - 43
31316C40 - 43
41316D40 - 43
11411A44
21411B44
31411C44
41411D44
11511A45 - 47
21511B45 - 47
31511C45 - 47
41511D45 - 47
11613A48 - 49
21613B48 - 49
31613C48 - 49
41613D48 - 49
11711A50
21711B50
31711C50
41711D50
11813A51
21813B51
31813C51
41813D51
11911A52 - 55
21911B52 - 55
31911C52 - 55
41911D52 - 55
12013A56 - 58
22013B56 - 58
32013C56 - 58
42013D56 - 58
12111A59
22111B59
32111C59
42111D59
12213A60
22213B60
32213C60
42213D60
12311A61 - 64
22311B61 - 64
32311C61 - 64
42311D61 - 64
12413A65 - 66
22413B65 - 66
32413C65 - 66
42413D65 - 66
12511A67 - 73
22511B67 - 73
32511C67 - 73
42511D67 - 73
12613A74
22613B74
32613C74
42613D74
12711A75 - 76
22711B75 - 76
32711C75 - 76
42711D75 - 76
12813A77
22813B77
32813C77
42813D77
12911A78 - 80
22911B78 - 80
32911C78 - 80
42911D78 - 80
13013A81
23013B81
33013C81
43013D81
13116A82 - 83
23116B82 - 83
33116C82 - 83
43116D82 - 83
13213A84
23213B84
33213C84
43213D84
13311A85 - 95
23311B85 - 95
33311C85 - 95
43311D85 - 95
13413A96 - 97
23413B96 - 97
33413C96 - 97
43413D96 - 97
13511A98
23511B98
33511C98
43511D98
13613A99
23613B99
33613C99
43613D99
13716A100
23716B100
33716C100
43716D100
13811A101
23811B101
33811C101
43811D101
13913A102 - 103
23913B102 - 103
33913C102 - 103
43913D102 - 103
14011A104 - 114
24011B104 - 114
34011C104 - 114
44011D104 - 114
1123A115
2123B115
3123C115
4123D115
1221A116
2221B116
3221C116
4221D116
1323A117 - 118
2323B117 - 118
3323C117 - 118
4323D117 - 118
1426A119 - 131
2426B119 - 131
3426C119 - 131
4426D119 - 131
1521A132 - 133
2521B132 - 133
3521C132 - 133
4521D132 - 133
1623A134 - 135
2623B134 - 135
3623C134 - 135
4623D134 - 135
1721A136 - 141
2721B136 - 141
3721C136 - 141
4721D136 - 141
1823A142
2823B142
3823C142
4823D142
1921A143 - 145
2921B143 - 145
3921C143 - 145
4921D143 - 145
11023A146 - 147
21023B146 - 147
31023C146 - 147
41023D146 - 147
11121A148 - 150
21121B148 - 150
31121C148 - 150
41121D148 - 150
11223A151
21223B151
31223C151
41223D151
11321A152 - 154
21321B152 - 154
31321C152 - 154
41321D152 - 154
11423A155 - 156
21423B155 - 156
31423C155 - 156
41423D155 - 156
11521A157 - 163
21521B157 - 163
31521C157 - 163
41521D157 - 163
11623A164
21623B164
31623C164
41623D164
11721A165 - 171
21721B165 - 171
31721C165 - 171
41721D165 - 171
11823A172
21823B172
31823C172
41823D172
11921A173 - 176
21921B173 - 176
31921C173 - 176
41921D173 - 176
12023A177
22023B177
32023C177
42023D177
12121A178 - 179
22121B178 - 179
32121C178 - 179
42121D178 - 179
12223A180 - 186
22223B180 - 186
32223C180 - 186
42223D180 - 186
12321A187 - 188
22321B187 - 188
32321C187 - 188
42321D187 - 188
12426A189 - 190
22426B189 - 190
32426C189 - 190
42426D189 - 190
12521A191 - 193
22521B191 - 193
32521C191 - 193
42521D191 - 193
12623A194
22623B194
32623C194
42623D194
12721A195 - 197
22721B195 - 197
32721C195 - 197
42721D195 - 197
12823A198
22823B198
32823C198
42823D198
12921A199
22921B199
32921C199
42921D199
13023A200
23023B200
33023C200
43023D200
13121A201 - 207
23121B201 - 207
33121C201 - 207
43121D201 - 207
13223A208 - 216
23223B208 - 216
33223C208 - 216
43223D208 - 216
13326A217
23326B217
33326C217
43326D217
13423A218 - 226
23423B218 - 226
33423C218 - 226
43423D218 - 226
13526A601
23526B601
33526C601
43526D601
13626A2647
23626B2647
33626A2647
43626D2647
13726A4849 - 4852
23726B - D4849 - 4852
33726C4849 - 4852
43726D4849 - 4852

NCS ensembles :
ID
1
2

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
protein GH61E


Mass: 22569.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (fungus) / Strain: NRLL 8126 / Gene: gh61e / Plasmid: pAlLo28 / Production host: Aspergillus oryzae (mold) / Strain (production host): JaL250 / References: UniProt: D0VWZ9*PLUS
#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.: 4
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

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Non-polymers , 4 types, 868 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M MgSO4, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.902→15 Å / Num. obs: 69834 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.094 / Net I/σ(I): 31
Reflection shellResolution: 1.902→1.97 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.483 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.902→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.965 / SU ML: 0.089 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20396 3449 5.1 %RANDOM
Rwork0.18428 ---
all0.1853 64309 --
obs0.1853 64309 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.959 Å2
Refinement stepCycle: LAST / Resolution: 1.902→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 127 851 7374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226841
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9469444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99524.474304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41115854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9871520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025464
X-RAY DIFFRACTIONr_nbd_refined0.1780.23037
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2816
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.246
X-RAY DIFFRACTIONr_mcbond_it0.5131.54305
X-RAY DIFFRACTIONr_mcangle_it0.92426858
X-RAY DIFFRACTIONr_scbond_it1.17533021
X-RAY DIFFRACTIONr_scangle_it1.8114.52584
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A583tight positional0.030.05
12B583tight positional0.030.05
13C583tight positional0.040.05
14D583tight positional0.030.05
21A559tight positional0.040.05
22B559tight positional0.040.05
23C559tight positional0.050.05
24D559tight positional0.040.05
11A147loose positional0.315
12B147loose positional0.335
13C147loose positional0.325
14D147loose positional0.355
21A268loose positional0.515
22B268loose positional0.475
23C268loose positional0.495
24D268loose positional0.375
11A583tight thermal0.10.5
12B583tight thermal0.150.5
13C583tight thermal0.110.5
14D583tight thermal0.080.5
21A559tight thermal0.090.5
22B559tight thermal0.110.5
23C559tight thermal0.090.5
24D559tight thermal0.070.5
11A147loose thermal1.5810
12B147loose thermal2.0210
13C147loose thermal1.3910
14D147loose thermal1.2710
21A268loose thermal2.5610
22B268loose thermal1.2510
23C268loose thermal1.3510
24D268loose thermal1.510
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 201 -
Rwork0.222 4661 -
obs--95.6 %

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