[English] 日本語
Yorodumi
- PDB-4e3v: Crystal Structure of XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e3v
TitleCrystal Structure of XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS Cryoprotected in Proline
ComponentsXylose isomerase
KeywordsISOMERASE
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
: / PROLINE / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsTanner, J.J. / Pemberton, T.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography.
Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6706
Polymers43,2831
Non-polymers3865
Water5,837324
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,67924
Polymers173,1334
Non-polymers1,54620
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 area32220 Å2
ΔGint-279 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.493, 98.022, 102.425
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-751-

HOH

21A-815-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Xylose isomerase /


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase

-
Non-polymers , 5 types, 329 molecules

#2: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.46 Å / Num. all: 72416 / Num. obs: 72416 / % possible obs: 99.6 %

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XIF

1xif


Resolution: 1.503→19.46 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 3657 5.05 %
Rwork0.1643 --
obs0.165 72403 97.72 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.605 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2973 Å2-0 Å20 Å2
2--1.7763 Å2-0 Å2
3----1.479 Å2
Refinement stepCycle: LAST / Resolution: 1.503→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 20 324 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063147
X-RAY DIFFRACTIONf_angle_d1.1074271
X-RAY DIFFRACTIONf_dihedral_angle_d12.3761166
X-RAY DIFFRACTIONf_chiral_restr0.07442
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.503-1.52270.4327980.33871834X-RAY DIFFRACTION68
1.5227-1.54350.36221270.27872567X-RAY DIFFRACTION95
1.5435-1.56560.24081320.23992625X-RAY DIFFRACTION97
1.5656-1.58890.22661400.19022585X-RAY DIFFRACTION97
1.5889-1.61370.17691340.15972610X-RAY DIFFRACTION98
1.6137-1.64020.16511470.14022622X-RAY DIFFRACTION98
1.6402-1.66850.1811380.14452629X-RAY DIFFRACTION98
1.6685-1.69880.15961390.14052650X-RAY DIFFRACTION98
1.6988-1.73140.17171350.1432667X-RAY DIFFRACTION99
1.7314-1.76670.17741440.13922643X-RAY DIFFRACTION99
1.7667-1.80510.14581390.14432659X-RAY DIFFRACTION99
1.8051-1.84710.15721330.14732667X-RAY DIFFRACTION99
1.8471-1.89320.16411240.15332666X-RAY DIFFRACTION99
1.8932-1.94440.17971280.15072663X-RAY DIFFRACTION99
1.9444-2.00160.18761430.16282693X-RAY DIFFRACTION99
2.0016-2.06610.16471600.15612662X-RAY DIFFRACTION99
2.0661-2.13980.17361600.16922662X-RAY DIFFRACTION100
2.1398-2.22540.17361490.15882712X-RAY DIFFRACTION100
2.2254-2.32650.17531660.15512662X-RAY DIFFRACTION100
2.3265-2.4490.17521520.15862692X-RAY DIFFRACTION100
2.449-2.60210.20421470.16992701X-RAY DIFFRACTION100
2.6021-2.80240.19891270.17832750X-RAY DIFFRACTION100
2.8024-3.08350.1921550.17952716X-RAY DIFFRACTION100
3.0835-3.52730.181490.16832765X-RAY DIFFRACTION100
3.5273-4.43540.13871540.14062763X-RAY DIFFRACTION100
4.4354-19.460.16651370.16932881X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.7345 Å / Origin y: 38.8119 Å / Origin z: 61.723 Å
111213212223313233
T0.0437 Å2-0.008 Å20.0116 Å2-0.0601 Å2-0.0022 Å2--0.0536 Å2
L0.1713 °20.0342 °20.0254 °2-0.194 °2-0.0032 °2--0.2736 °2
S-0.0053 Å °-0.0253 Å °-0.0206 Å °0.0219 Å °-0.0095 Å °0.028 Å °0.0342 Å °-0.05 Å °0.0144 Å °
Refinement TLS groupSelection details: Chain A and resseq 3:387

+
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