[English] 日本語
Yorodumi
- PDB-1a0e: XYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a0e
TitleXYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA
ComponentsXYLOSE ISOMERASE
KeywordsKETOLISOMERASE / XYLOSE METABOLISM / GLUCOSE-FRUCTOSE INTERCONVERSION / HYDRIDE TRANSFER / ALPHA-BETA BARREL / METALLOENZYME / THERMOPHILE
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, bacterial-type / 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
: / Xylose isomerase
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGallay, O. / Chopra, R. / Conti, E. / Brick, P. / Blow, D.
Citation
Journal: To be Published
Title: Crystal Structures of Class II Xylose Isomerases from Two Thermophiles and a Hyperthermophile
Authors: Gallay, O. / Chopra, R. / Conti, E. / Brick, P. / Jackson, R. / Hartley, B. / Vieille, C. / Zeikus, J.G. / Blow, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Initial X-Ray Analysis of Xylose Isomerase from Thermotoga Neapolitana
Authors: Chayen, N.E. / Conti, E. / Vieille, C. / Zeikus, J.G.
#2: Journal: Appl.Environ.Microbiol. / Year: 1995
Title: Xyla Cloning and Sequencing and Biochemical Characterization of Xylose Isomerase from Thermotoga Neapolitana
Authors: Vieille, C. / Hess, J.M. / Kelly, R.M. / Zeikus, J.G.
History
DepositionNov 28, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,0178
Polymers101,6632
Non-polymers3546
Water4,612256
1
A: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,03416
Polymers203,3264
Non-polymers70712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area30610 Å2
ΔGint-287 kcal/mol
Surface area55690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)161.790, 121.870, 98.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-493-

CO

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, 0.00298, 0.0021), (-0.00259, -0.98577, 0.16811), (0.00257, 0.1681, 0.98577)
Vector: 80.53531, 0.16098, -0.04196)

-
Components

#1: Protein XYLOSE ISOMERASE / GLUCOSE ISOMERASE


Mass: 50831.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Strain: 5068 / Cellular location: CYTOPLASM / Gene: XYLA / Plasmid: PTNE2 / Cellular location (production host): CYTOPLASM / Gene (production host): XYLA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P45687, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 14% JEFFAMINE ED 4000, 5 MM MGSO4, 0.5 MM COCL2, 50 MM MOPS, PH 7.0 (FOR DETAILS SEE REFERENCE 1).

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 1, 1994 / Details: DUAL SLIT, COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→12.5 Å / Num. obs: 26137 / % possible obs: 96.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.3 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XYLOSE ISOMERASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES

Resolution: 2.7→12.5 Å / Rfactor Rfree error: 0.006 / Cross valid method: A POSTERIORI
Details: DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1265 5 %RANDOM
Rwork0.18 ---
obs0.18 26119 97.1 %-
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 6 256 7274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 144 5 %
Rwork0.288 2957 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM.IONTOPH.ION

+
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