[English] 日本語
Yorodumi
- PDB-3fcy: Crystal Structure of Acetyl Xylan Esterase 1 from Thermoanaerobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fcy
TitleCrystal Structure of Acetyl Xylan Esterase 1 from Thermoanaerobacterium sp. JW/SL YS485
ComponentsXylan esterase 1
KeywordsHYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Thermoanaerobacterium sp.
Function / homology
Function and homology information


polysaccharide metabolic process / carboxylic ester hydrolase activity / metal ion binding
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoanaerobacterium sp. 'JW/SL YS485' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKrastanova, I. / Cassetta, A. / Lamba, D.
Citation
Journal: To be Published
Title: Crystal Structure Analysis of Acetyl Xylan Esterase 1 from Thermoanaerobacterium sp. JW/SL YS485
Authors: Krastanova, I. / Cassetta, A. / Wiegel, J. / Lamba, D.
#1: Journal: APPL.ENVIRON.MICROBIOL. / Year: 1995
Title: Purification and Characterization of Two Thermostable Acetyl Xylan Esterases from Thermoanaerobacterium sp. Strain JW/SL-YS485
Authors: Shao, W. / Wiegel, J.
#2: Journal: J.BACTERIOL. / Year: 1997
Title: Isolation, Analysis, and Expression of Two Genes from Thermoanaerobacterium sp. Strain JW/SL YS485: a beta-Xylosidase and a Novel Acetyl Xylan Esterase with Cephalosporin C Deacetylase Activity
Authors: Lorenz, W.W. / Wiegel, J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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_ref_seq_dif / struct_site
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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1955
Polymers118,1153
Non-polymers802
Water8,809489
1
A: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules

A: Xylan esterase 1
B: Xylan esterase 1
C: Xylan esterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,38910
Polymers236,2296
Non-polymers1604
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area15970 Å2
ΔGint-55 kcal/mol
Surface area60200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.263, 132.263, 112.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-321-

CA

-
Components

#1: Protein Xylan esterase 1


Mass: 39371.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium sp. 'JW/SL YS485' (bacteria)
Strain: JW/SL YS485 / Gene: axe1 / Plasmid: modified pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: O30361, acetylxylan esterase, cephalosporin-C deacetylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 14% PEG 400, 0.1M calcium chloride, 0.05M sodium HEPES, pH 7.5, microbatch, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 66742 / Num. obs: 66742 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.01
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3296 / Χ2: 0.972 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å25 Å
Translation3.5 Å25 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FVR

3fvr


Resolution: 2.1→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6761 10.1 %RANDOM
Rwork0.184 ---
all0.184 66710 --
obs0.184 66710 100 %-
Solvent computationBsol: 53.972 Å2
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 28 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.705 Å20.702 Å20 Å2
2--2.705 Å20 Å2
3----5.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 2 489 8063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_mcbond_it1.1241.5
X-RAY DIFFRACTIONc_scbond_it1.9832
X-RAY DIFFRACTIONc_mcangle_it1.5842
X-RAY DIFFRACTIONc_scangle_it2.8942.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
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