[English] 日本語
Yorodumi
- PDB-12ny: Crystal structure of a GH26 enzyme (EiGH26b) in complex with mannose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12ny
TitleCrystal structure of a GH26 enzyme (EiGH26b) in complex with mannose
ComponentsGlycoside hydrolase family 26
KeywordsHYDROLASE / metagenome / manatee / gut microbiota / heteromannan
Function / homologybeta-D-mannopyranose / alpha-D-mannopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsOliveira, C.H.M. / Miyamoto, R.Y. / Noske, G.D. / Martins, M.P. / Murakami, M.T.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2022/03059-5 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303898/2024-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)304440/2024-8 Brazil
CitationJournal: To Be Published
Title: Crystal structure of a GH26 enzyme (EiGH26b) in complex with mannose
Authors: Persinoti, G.F. / Martins, M.P. / Silva, C.B.C. / Streit, R.S.A. / Paixao, D.A.A. / Martins, G.H. / Higasi, P.M.R. / Braatz, G.M. / Silva, M.K.P. / Morao, L.G. / Martins-Junior, J. / ...Authors: Persinoti, G.F. / Martins, M.P. / Silva, C.B.C. / Streit, R.S.A. / Paixao, D.A.A. / Martins, G.H. / Higasi, P.M.R. / Braatz, G.M. / Silva, M.K.P. / Morao, L.G. / Martins-Junior, J. / Stoffel, F. / Ciol, H. / Noske, G.D. / Miyamoto, R.Y. / Oliveira, G.M. / Martim, D.B. / Oliveira, C.H.M. / Almeida, O.A.C. / Araujo, E.A. / Andrade, M.O. / Santos, C.A. / Diogo, J.A. / Wolf, L.D. / Zanotto, J.V. / Souza, A.R. / Goncalves, F.A.C. / Mello, D.M.D. / Morais, M.A.B. / Porto, J. / Lombard, V. / Giuseppe, P.O. / Terrapon, N. / Lemos, L.N. / Henrissat, B. / Carvalho, V.L. / Silva, V.M.F. / Murakami, M.T.
History
DepositionApr 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase family 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7774
Polymers35,2361
Non-polymers5403
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.007, 87.007, 85.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1219-

HOH

-
Components

#1: Protein Glycoside hydrolase family 26


Mass: 35236.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium Acetate 4.6 pH, 2 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.71→43.5 Å / Num. obs: 35159 / % possible obs: 68.7 % / Redundancy: 13.08 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.113 / Net I/σ(I): 6.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.71-1.820.840030.4011.0491
1.82-1.940.50139860.6480.6541
1.94-2.10.27635850.8610.3591
2.1-2.30.18233250.9430.2351
2.3-2.570.12629590.9720.1621
2.57-2.960.08224750.9870.1051
2.96-3.630.0520350.9950.0631
3.63-5.110.03114620.9970.0381
5.11-43.50.0327660.9980.0381

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→43.5 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 1758 5 %
Rwork0.175 --
obs0.1763 35159 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 36 97 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162451
X-RAY DIFFRACTIONf_angle_d1.3073342
X-RAY DIFFRACTIONf_dihedral_angle_d21.446873
X-RAY DIFFRACTIONf_chiral_restr0.083381
X-RAY DIFFRACTIONf_plane_restr0.011422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.29961240.26532366X-RAY DIFFRACTION93
1.76-1.810.25321310.2382491X-RAY DIFFRACTION97
1.81-1.870.28281330.2352518X-RAY DIFFRACTION98
1.87-1.940.24361320.19882521X-RAY DIFFRACTION98
1.94-2.020.18921330.16832527X-RAY DIFFRACTION99
2.02-2.110.20121350.15832562X-RAY DIFFRACTION99
2.11-2.220.19241350.16212551X-RAY DIFFRACTION99
2.22-2.360.21931340.16422559X-RAY DIFFRACTION99
2.36-2.540.19881360.16682589X-RAY DIFFRACTION99
2.54-2.790.19371370.16422594X-RAY DIFFRACTION99
2.79-3.20.21241380.17592630X-RAY DIFFRACTION99
3.2-4.030.18981410.15722661X-RAY DIFFRACTION100
4.03-43.50.18011490.18042832X-RAY DIFFRACTION100
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)
10.1391-0.23740.0211.3176-0.18890.0410.15090.1650.3298-0.3318-0.2672-0.74160.01130.1417-0.01520.16740.00840.04280.21950.00440.2231-5.9648-31.0429-13.5373
20.3379-0.42770.15450.5248-0.19720.1832-0.0495-0.08530.04460.05720.014-0.1099-0.04440.0789-0.00010.171-0.0113-0.00580.2193-0.02310.2031-12.3399-26.7113.2091
30.95840.08530.15680.55620.0030.25940.0296-0.08140.04160.0402-0.0199-0.0157-0.03350.016600.1581-0.0052-0.00740.1693-0.01310.1463-30.4059-27.2663-2.9834
40.4232-0.4845-0.16210.59880.30480.38140.02340.0503-0.14040.0208-0.07210.01720.05650.0112-0.00010.1555-0.0025-0.01060.1783-0.00830.1517-26.9709-35.2373-9.1812
51.21660.25940.31770.31070.4130.8040.035-0.0035-0.26380.00310.01430.00690.1422-0.08760.00010.19410.01250.00180.1741-0.0060.199-17.3018-47.1419-4.7701
60.47090.36420.240.52310.14250.12940.0677-0.2037-0.2087-0.0223-0.0359-0.03280.09710.10230.00290.1540.02380.00730.22260.02320.2574-7.8638-44.70573.4177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 715 through 731 )
2X-RAY DIFFRACTION2chain 'A' and (resid 732 through 791 )
3X-RAY DIFFRACTION3chain 'A' and (resid 792 through 861 )
4X-RAY DIFFRACTION4chain 'A' and (resid 862 through 920 )
5X-RAY DIFFRACTION5chain 'A' and (resid 921 through 990 )
6X-RAY DIFFRACTION6chain 'A' and (resid 991 through 1021 )

+
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