[English] 日本語
Yorodumi
- PDB-4xia: STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xia
TitleSTRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY
ComponentsD-XYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
sorbitol / Xylose isomerase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHenrick, K. / Collyer, C.A. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively.
Authors: Henrick, K. / Collyer, C.A. / Blow, D.M.
#1: Journal: Protein Eng. / Year: 1987
Title: Comparison of Backbone Structures of Glucose Isomerase from Streptomyces and Arthrobacter
Authors: Henrick, K. / Blow, D.M. / Carrell, H.L. / Glusker, J.P.
#2: Journal: Biochim.Biophys.Acta / Year: 1986
Title: The Crystallization of Glucose Isomerase from Arthrobacter B3728
Authors: Akins, J. / Brick, P. / Jones, H.B. / Hirayama, N. / Shaw, P.-C. / Blow, D.M.
History
DepositionJul 5, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE TWO SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT- ...SHEET THE TWO SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. EACH IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3096
Polymers85,8962
Non-polymers4134
Water9,692538
1
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,61712
Polymers171,7914
Non-polymers8268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area34000 Å2
ΔGint-175 kcal/mol
Surface area44350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.800, 105.800, 153.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUES PRO A 186 AND PRO B 186 ARE CIS PROLINES.
2: THE CD-NE-CZ ANGLE OF ARG A 158 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8839, -0.0648, 0.4632), (-0.0706, -0.9605, -0.269), (0.4624, -0.2705, 0.8444)
Vector: 66.28, 115.1, 0.16)

-
Components

#1: Protein D-XYLOSE ISOMERASE


Mass: 42947.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: NRRL B3728 / References: UniProt: P12070, xylose isomerase
#2: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: Akins, J., (1986) Biochim.Biophys.Acta, 874, 375.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
21.2 Mammonium sulfate1drop
350 mMTris-acetate1reservoir
410 mM1reservoirMgCl2

-
Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 44186 / % possible obs: 98.8 % / Num. measured all: 127622 / Rmerge(I) obs: 0.062

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→6 Å
Details: THE CD-NE-CZ ANGLE OF ARG A 158 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
RfactorNum. reflection
obs0.147 41617
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 26 538 6618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.911.5
X-RAY DIFFRACTIONp_mcangle_it1.462
X-RAY DIFFRACTIONp_scbond_it1.952
X-RAY DIFFRACTIONp_scangle_it2.983
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.2
X-RAY DIFFRACTIONp_multtor_nbd0.220.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 43615 / Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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