[English] 日本語
Yorodumi
- PDB-2gub: Crystal Structure of Metal Free D-Xylose Isomerase. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gub
TitleCrystal Structure of Metal Free D-Xylose Isomerase.
ComponentsXylose isomerase
KeywordsISOMERASE / TIM barrel / beta-alpha-barrel / metal-free / inactive enzyme / sugar interconversion
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein 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
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCarrell, H.L. / Katz, A.K. / Glusker, J.P.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.
Authors: Katz, A.K. / Li, X. / Carrell, H.L. / Hanson, B.L. / Langan, P. / Coates, L. / Schoenborn, B.P. / Glusker, J.P. / Bunick, G.J.
#1: Journal: To be Published
Title: Structural studies of D-Xylose isomerase and metal binding.
Authors: Carrell, H.L. / Katz, A.K. / Glusker, J.P.
History
DepositionApr 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)43,2831
Polymers43,2831
Non-polymers00
Water6,738374
1
A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)173,1334
Polymers173,1334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area30320 Å2
ΔGint-101 kcal/mol
Surface area46050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.800, 99.500, 102.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21A-660-

HOH

31A-712-

HOH

Detailshomo-tetramer consisting of subunits related by crystallographic 222 symmetry.

-
Components

#1: Protein Xylose isomerase /


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Purified enzyme obtained as gift from Clinton Corn Products, Clinton, Ia.
Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 279 K / Method: small tubes / pH: 8
Details: Crystallization from solution containing metal free enzyme at 20 mg/ml, 0.8M AmSO4, 2mM Pipes. Crystallization occurred over 2 day period in sealed tubes., pH 8.0, SMALL TUBES, temperature 279K

-
Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Nov 15, 1995 / Details: focussing nickel mirrors
RadiationMonochromator: Focussed Ni Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→70.71 Å / Num. obs: 40569 / % possible obs: 0.83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.9 Å / % possible all: 86.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DATCOLdata reduction
XDSdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1XIB without metal ions and solvent

1xib


Resolution: 1.8→70.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.119 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19327 2121 5 %RANDOM
Rwork0.15958 ---
obs0.16124 40237 93.79 %-
all-40569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 374 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9524207
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46522.976168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951535
X-RAY DIFFRACTIONr_chiral_restr0.1520.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21339
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.273
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2351.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80223026
X-RAY DIFFRACTIONr_scbond_it3.28131295
X-RAY DIFFRACTIONr_scangle_it5.1924.51181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 141 -
Rwork0.289 2578 -
obs-2578 82.39 %

+
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