[English] 日本語
Yorodumi
- PDB-4xuy: Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrola... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xuy
TitleCrystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Aspergillus niger
ComponentsProbable endo-1,4-beta-xylanase C
KeywordsHYDROLASE / xylanase / GH10 / glycoside hydrolase family 10 / fungus / genomics / beta8/alpha8 fold / TIM barrel
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Probable endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.0027 Å
AuthorsStogios, P.J. / Dong, A. / Xu, X. / Cui, H. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of an endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Aspergillus niger
Authors: Stogios, P.J. / Dong, A. / Xu, X. / Cui, H. / Savchenko, A.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable endo-1,4-beta-xylanase C
B: Probable endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2069
Polymers65,5572
Non-polymers6497
Water11,367631
1
A: Probable endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0554
Polymers32,7791
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable endo-1,4-beta-xylanase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1515
Polymers32,7791
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.585, 50.685, 59.097
Angle α, β, γ (deg.)83.19, 87.31, 61.66
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 32778.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: CBS 513.88 / FGSC A1513 / Gene: xlnC, xynA, An03g00940 / Plasmid: ANIp7G / Production host: Aspergillus niger (mold) / Strain (production host): BL21 (DE3) / References: UniProt: A2QFV7, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 2.5 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 32566 / % possible obs: 94.9 % / Redundancy: 3.8 % / Rsym value: 0.121 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 2.05 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B30

1b30


Resolution: 2.0027→29.338 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1654 5.08 %Random selection
Rwork0.1412 ---
obs0.1444 32555 94.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0027→29.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 41 631 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084789
X-RAY DIFFRACTIONf_angle_d1.1236510
X-RAY DIFFRACTIONf_dihedral_angle_d12.661702
X-RAY DIFFRACTIONf_chiral_restr0.077723
X-RAY DIFFRACTIONf_plane_restr0.005831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0027-2.06160.2341030.17752343X-RAY DIFFRACTION85
2.0616-2.12810.23511280.15352533X-RAY DIFFRACTION92
2.1281-2.20410.21411390.13852543X-RAY DIFFRACTION93
2.2041-2.29240.24421540.15552525X-RAY DIFFRACTION93
2.2924-2.39670.2461230.14652549X-RAY DIFFRACTION94
2.3967-2.52290.2461340.14042589X-RAY DIFFRACTION94
2.5229-2.68090.19891290.14192596X-RAY DIFFRACTION95
2.6809-2.88770.19691530.13852603X-RAY DIFFRACTION96
2.8877-3.1780.20071350.13112635X-RAY DIFFRACTION96
3.178-3.63720.17891480.12892623X-RAY DIFFRACTION97
3.6372-4.57960.1641560.1212681X-RAY DIFFRACTION98
4.5796-29.34160.20921520.16682681X-RAY DIFFRACTION99
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)
11.9325-1.5649-0.74371.78050.70380.9101-0.00990.0894-0.1371-0.0536-0.01960.17120.0285-0.01860.02390.1245-0.0084-0.00510.12870.01160.11839.925984.6129-42.456
21.11340.0764-0.38620.51130.09410.56130.0269-0.10980.03120.0297-0.0043-0.07980.00330.1107-0.01960.11950.0071-0.00020.116-0.00260.131830.386594.023-33.7448
31.41090.40430.10280.8742-0.03520.89790.0226-0.15810.0280.05050.0260.04850.0127-0.0686-0.04850.10750.01680.00160.13830.01180.11513.407590.003-27.6678
40.74440.19180.03330.9553-0.20440.43640.0058-0.0079-0.03590.0250.02250.01750.0216-0.0098-0.02980.1260.00270.01070.1035-0.00190.0964-3.0375104.7717-52.2478
51.48870.3121-0.25930.6581-0.26650.771-0.00370.19030.0089-0.13340.03770.05790.0504-0.0873-0.03650.15880.0033-0.01550.12460.00090.1139-6.0399110.1478-68.1531
61.7388-0.97070.30311.8271-0.6531.17430.0297-0.040.0005-0.1095-0.0248-0.15450.0880.1183-0.00070.122-0.01030.00770.1224-0.02640.129812.6186114.6746-59.1158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 26:68
2X-RAY DIFFRACTION2chain A and resi 69:180
3X-RAY DIFFRACTION3chain A and resi 181:327
4X-RAY DIFFRACTION4chain B and resi 26:156
5X-RAY DIFFRACTION5chain B and resi 157:271
6X-RAY DIFFRACTION6chain B and resi 272:327

+
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://pdbjlvh1.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