[English] 日本語
Yorodumi
- PDB-6d25: Crystal structure of the GH51 arabinofuranosidase from Xanthomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d25
TitleCrystal structure of the GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri
ComponentsAlpha-L-arabinosidase
KeywordsHYDROLASE / arabinofuranosidase / di-substitution recognition / GH51 / enzyme / trimer
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Alpha-L-arabinosidase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsSantos, C.R. / Morais, M.A.B. / Tonoli, C.C.C. / Giuseppe, P.O. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/13309-0, 2014/07135-1 , 2015/26982-0 Brazil
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans.
Authors: Dos Santos, C.R. / de Giuseppe, P.O. / de Souza, F.H.M. / Zanphorlin, L.M. / Domingues, M.N. / Pirolla, R.A.S. / Honorato, R.V. / Tonoli, C.C.C. / de Morais, M.A.B. / de Matos Martins, V.P. ...Authors: Dos Santos, C.R. / de Giuseppe, P.O. / de Souza, F.H.M. / Zanphorlin, L.M. / Domingues, M.N. / Pirolla, R.A.S. / Honorato, R.V. / Tonoli, C.C.C. / de Morais, M.A.B. / de Matos Martins, V.P. / Fonseca, L.M. / Buchli, F. / de Oliveira, P.S.L. / Gozzo, F.C. / Murakami, M.T.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-L-arabinosidase
B: Alpha-L-arabinosidase
C: Alpha-L-arabinosidase
D: Alpha-L-arabinosidase
E: Alpha-L-arabinosidase
F: Alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,76712
Polymers343,2146
Non-polymers5536
Water42,9482384
1
A: Alpha-L-arabinosidase
B: Alpha-L-arabinosidase
C: Alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8836
Polymers171,6073
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-12 kcal/mol
Surface area50470 Å2
MethodPISA
2
D: Alpha-L-arabinosidase
E: Alpha-L-arabinosidase
F: Alpha-L-arabinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8836
Polymers171,6073
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-12 kcal/mol
Surface area50530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.344, 163.231, 114.425
Angle α, β, γ (deg.)90.000, 107.570, 90.000
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA8 - 49928 - 519
21GLUGLULEULEUBB8 - 49928 - 519
12GLUGLULEULEUAA8 - 49928 - 519
22GLUGLULEULEUCC8 - 49928 - 519
13GLUGLULEULEUAA8 - 49928 - 519
23GLUGLULEULEUDD8 - 49928 - 519
14ALAALALEULEUAA6 - 49926 - 519
24ALAALALEULEUEE6 - 49926 - 519
15GLUGLULEULEUAA8 - 49928 - 519
25GLUGLULEULEUFF8 - 49928 - 519
16GLUGLUGLNGLNBB8 - 50028 - 520
26GLUGLUGLNGLNCC8 - 50028 - 520
17GLUGLUGLNGLNBB8 - 50028 - 520
27GLUGLUGLNGLNDD8 - 50028 - 520
18GLUGLULEULEUBB8 - 49928 - 519
28GLUGLULEULEUEE8 - 49928 - 519
19GLUGLUGLNGLNBB8 - 50028 - 520
29GLUGLUGLNGLNFF8 - 50028 - 520
110GLUGLUGLNGLNCC8 - 50028 - 520
210GLUGLUGLNGLNDD8 - 50028 - 520
111GLUGLULEULEUCC8 - 49928 - 519
211GLUGLULEULEUEE8 - 49928 - 519
112GLUGLUGLNGLNCC8 - 50028 - 520
212GLUGLUGLNGLNFF8 - 50028 - 520
113GLUGLULEULEUDD8 - 49928 - 519
213GLUGLULEULEUEE8 - 49928 - 519
114GLUGLUGLNGLNDD8 - 50028 - 520
214GLUGLUGLNGLNFF8 - 50028 - 520
115GLUGLULEULEUEE8 - 49928 - 519
215GLUGLULEULEUFF8 - 49928 - 519

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

-
Components

#1: Protein
Alpha-L-arabinosidase


Mass: 57202.371 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC1286 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: Q8PMY9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 2384 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 17% (w/v) polyethylene glycol 3350 and 0.2 M ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→48.74 Å / Num. obs: 236094 / % possible obs: 95.1 % / Redundancy: 3.429 % / Biso Wilson estimate: 28.412 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.113 / Χ2: 1.003 / Net I/σ(I): 9.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.91-2.032.810.5142.06633910.7290.63980.3
2.03-2.173.5290.3763.55731490.8760.44698.4
2.17-2.343.4910.2595.05676130.9380.30797.7
2.34-2.563.5440.1866.74627230.9660.2298.6
2.56-2.863.5020.1279.35560570.9820.15197.4
2.86-3.33.5790.07814.35499260.9930.09398.4
3.3-4.043.4930.05220.82416750.9960.06297.2
4.04-5.73.5240.04224.77324530.9970.0597.4
5.7-48.743.6140.04325.62180120.9970.05197.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VRQ

2vrq


Resolution: 1.91→48.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.216 / SU ML: 0.079 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1667 2000 0.8 %RANDOM
Rwork0.1487 ---
obs0.1488 234093 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.19 Å2 / Biso mean: 23.528 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.22 Å2
2---0.22 Å20 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.91→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23035 0 36 2384 25455
Biso mean--23.05 30.75 -
Num. residues----2964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01523755
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720843
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.75432403
X-RAY DIFFRACTIONr_angle_other_deg0.5271.69848770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56452958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06619.81949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.501153191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.20315147
X-RAY DIFFRACTIONr_chiral_restr0.0730.23059
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02127068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024497
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A166380.06
12B166380.06
21A166660.05
22C166660.05
31A166250.06
32D166250.06
41A166420.06
42E166420.06
51A166290.06
52F166290.06
61B167040.06
62C167040.06
71B166850.06
72D166850.06
81B165800.06
82E165800.06
91B167100.06
92F167100.06
101C168490.05
102D168490.05
111C166250.06
112E166250.06
121C166940.06
122F166940.06
131D166520.06
132E166520.06
141D166590.06
142F166590.06
151E165250.07
152F165250.07
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 115 -
Rwork0.23 13459 -
all-13574 -
obs--74.73 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5823-0.2058-0.00910.5261-0.06280.38970.0145-0.0621-0.0591-0.01230.0108-0.01820.03130.0288-0.02530.0315-0.0152-0.02630.04720.00110.0836-3.977-12.6816.82
20.34640.0790.1280.51620.07430.5604-0.019-0.01230.0303-0.00720.0121-0.0162-0.0487-0.00550.00680.00630.0021-0.00130.0483-0.00130.079-0.42240.63221.388
30.7162-0.0276-0.29160.2218-0.0410.5526-0.02390.0178-0.0441-0.0146-0.00750.030.0289-0.05970.03130.02740.0029-0.02180.0689-0.00740.0909-48.78416.85924.536
40.61060.0515-0.11420.31650.12770.6151-0.02390.0706-0.0146-0.00170.034-0.05560.0420.0837-0.01020.03660.0033-0.03050.0897-0.00760.0923-2.55918.089-39.042
50.56950.25750.38130.62390.10160.86650.0633-0.036-0.1102-0.01050.06040.10150.1325-0.1494-0.12380.0889-0.0152-0.06660.11030.04090.1932-46.607-12.229-33.5
60.4614-0.25840.09740.6-0.08870.5845-0.031-0.0496-0.0030.01420.0089-0.0004-0.0686-0.09030.02220.01640.024-0.01560.114-0.01450.078-50.67641.889-35.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 500
2X-RAY DIFFRACTION2B8 - 500
3X-RAY DIFFRACTION3C8 - 500
4X-RAY DIFFRACTION4D8 - 500
5X-RAY DIFFRACTION5E6 - 500
6X-RAY DIFFRACTION6F8 - 500

+
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