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- PDB-4xup: Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Pa... -

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Basic information

Entry
Database: PDB / ID: 4xup
TitleStructure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C
ComponentsEndo-1,4-beta-xylanase C
KeywordsSUGAR BINDING PROTEIN / Binding Site / Carbohydrates / Enzyme Stability / Substrate Specificity / Endo-1 / 4-beta-xylanase / Xylan-binding domain / Thermophilic enzymes / Thermostabilizing Domains
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding
Similarity search - Function
Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 ...Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSainz-Polo, M.A. / Sanz-Aparicio, J.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Exploring Multimodularity in Plant Cell Wall Deconstruction: STRUCTURAL AND FUNCTIONAL ANALYSIS OF Xyn10C CONTAINING THE CBM22-1-CBM22-2 TANDEM.
Authors: Sainz-Polo, M.A. / Gonzalez, B. / Menendez, M. / Pastor, F.I. / Sanz-Aparicio, J.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barcinonensis xylanase 10C containing the CBM22-1-CBM22-2 tandem.
Authors: Sainz-Polo, M.A. / Gonzalez, B. / Pastor, F.I. / Sanz-Aparicio, J.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase C
B: Endo-1,4-beta-xylanase C
C: Endo-1,4-beta-xylanase C
D: Endo-1,4-beta-xylanase C
E: Endo-1,4-beta-xylanase C
F: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,99418
Polymers219,4096
Non-polymers58512
Water54030
1
A: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6483
Polymers36,5681
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7404
Polymers36,5681
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6082
Polymers36,5681
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7404
Polymers36,5681
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6082
Polymers36,5681
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6483
Polymers36,5681
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.170, 110.359, 118.522
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHRAA2 - 3322 - 332
21ALAALATHRTHRBB2 - 3322 - 332
12SERSERPROPROAA3 - 1603 - 160
22SERSERPROPROCC3 - 1603 - 160
13ALAALATHRTHRAA2 - 3322 - 332
23ALAALATHRTHRDD2 - 3322 - 332
14ALAALAGLUGLUAA4 - 1614 - 161
24ALAALAGLUGLUEE4 - 1614 - 161
15ALAALATHRTHRAA2 - 3322 - 332
25ALAALATHRTHRFF2 - 3322 - 332
16SERSERPROPROBB3 - 1603 - 160
26SERSERPROPROCC3 - 1603 - 160
17ALAALATHRTHRBB2 - 3322 - 332
27ALAALATHRTHRDD2 - 3322 - 332
18ALAALAGLUGLUBB4 - 1614 - 161
28ALAALAGLUGLUEE4 - 1614 - 161
19ALAALATHRTHRBB2 - 3322 - 332
29ALAALATHRTHRFF2 - 3322 - 332
110SERSERPROPROCC3 - 1603 - 160
210SERSERPROPRODD3 - 1603 - 160
111ALAALAPROPROCC4 - 1604 - 160
211ALAALAPROPROEE4 - 1604 - 160
112SERSERPROPROCC3 - 1603 - 160
212SERSERPROPROFF3 - 1603 - 160
113ALAALAGLNGLNDD4 - 1714 - 171
213ALAALAGLUGLUEE4 - 1614 - 161
114ALAALATHRTHRDD2 - 3322 - 332
214ALAALATHRTHRFF2 - 3322 - 332
115ALAALAGLUGLUEE4 - 1614 - 161
215ALAALAGLUGLUFF4 - 1614 - 161

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Endo-1,4-beta-xylanase C / Xylanase C / 1 / 4-beta-D-xylan xylanohydrolase C


Mass: 36568.238 Da / Num. of mol.: 6 / Fragment: UNP residues 28-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: xynC / Plasmid: pGEX-4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69230, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 23% PEG 3350, 0.2 M Calcium chloride, 0.1 M Bis Tris propane pH 5.5 Additive: 2% 1,6-Hexanediol Ratio (protein/precipitant/additive): 0.5/2/0.3 with streak seeding starting from spherulites.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979235 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2013
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979235 Å / Relative weight: 1
ReflectionResolution: 2.43→118.52 Å / Num. obs: 81116 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 37.24 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.085 / Net I/av σ(I): 4.8 / Net I/σ(I): 8.6 / Num. measured all: 510618
Reflection shellResolution: 2.43→2.48 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5568 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYO and 2w5f

1dyo

2w5f


Resolution: 2.43→118.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.54 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26495 4072 5 %RANDOM
Rwork0.22687 ---
obs0.22879 77022 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-1.17 Å2
2---2.43 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.43→118.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12488 0 22 30 12540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912732
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211801
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.94317274
X-RAY DIFFRACTIONr_angle_other_deg1.967327187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98551605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58725.441601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.507152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0231554
X-RAY DIFFRACTIONr_chiral_restr0.0790.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214699
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022871
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5644.7126450
X-RAY DIFFRACTIONr_mcbond_other3.5634.7116449
X-RAY DIFFRACTIONr_mcangle_it5.4077.0598045
X-RAY DIFFRACTIONr_mcangle_other5.4077.068046
X-RAY DIFFRACTIONr_scbond_it4.1045.0436282
X-RAY DIFFRACTIONr_scbond_other4.1035.0436282
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3597.4039230
X-RAY DIFFRACTIONr_long_range_B_refined8.41536.66313310
X-RAY DIFFRACTIONr_long_range_B_other8.41536.66513310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A371900.09
12B371900.09
21A179180.11
22C179180.11
31A371280.1
32D371280.1
41A182520.09
42E182520.09
51A374380.09
52F374380.09
61B178760.11
62C178760.11
71B381380.07
72D381380.07
81B183280.09
82E183280.09
91B380620.07
92F380620.07
101C179120.11
102D179120.11
111C179260.11
112E179260.11
121C179440.11
122F179440.11
131D182280.1
132E182280.1
141D379080.08
142F379080.08
151E182140.1
152F182140.1
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 263 -
Rwork0.342 5705 -
obs--99.3 %

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