[English] 日本語
Yorodumi
- PDB-1aw2: TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aw2
TitleTRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / PSYCHROPHILIC / VIBRIO MARINUS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glycerol catabolic process / glyceraldehyde-3-phosphate biosynthetic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMaes, D. / Zeelen, J.P. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.
Authors: Alvarez, M. / Zeelen, J.P. / Mainfroid, V. / Rentier-Delrue, F. / Martial, J.A. / Wyns, L. / Wierenga, R.K. / Maes, D.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,51412
Polymers214,1308
Non-polymers3844
Water3,099172
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18970 Å2
MethodPISA
3
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
4
J: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6283
Polymers53,5322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.660, 137.820, 89.540
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.007, 0.006, 1), (0.004, 1, -0.006), (-1, 0.004, 0.007)-0.85298, 34.55416, 88.58136
2given(1, -0.003, 0.01), (-0.004, -1, 0.006), (0.01, -0.006, -1)-0.49083, 102.28472, 88.97144
3given(-0.016, 1), (-1), (1, 0.016)0.02818, 67.90625, 0.01734

-
Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE


Mass: 26766.199 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: A SULFATE MOLECULE IS OBSERVED IN THE ACTIVE SITE OF SUBUNIT A
Source: (gene. exp.) Moritella marina (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P50921, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growpH: 7
Details: 100MM TRIETHANOLAMINE/HCL 100MM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 1.26M SODIUM CITRATE PH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMtriethanolamine-HCl1reservoir
325 mM1reservoirNaCl
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
61 mM1reservoirNaN3
720 mM2PG1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: DOUBLE FOCUSSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 60048 / % possible obs: 95.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 6.7 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 166818
Reflection shell
*PLUS
% possible obs: 95.8 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LIGANDED STRUCTURE (PDB ENTRY 1AFI)

1afi


Resolution: 2.65→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -5 %RANDOM
Rwork0.2 ---
obs0.2 57974 95.7 %-
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 5 43 3781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 -5 %
Rwork0.29 6576 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64
LS refinement shell
*PLUS
Rfactor obs: 0.29

+
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