[English] 日本語
Yorodumi
- PDB-4otb: 4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, RHOMBOHE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4otb
Title4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, RHOMBOHEDRAL CRYSTAL FORM
Components4-OXALOCROTONATE TAUTOMERASE
KeywordsISOMERASE / TAUTOMERASE / MICROBIAL BIODEGRADATION
Function / homology
Function and homology information


xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTaylor, A.B. / Whitman, C.P. / Hackert, M.L.
Citation
Journal: Thesis / Year: 1998
Title: Native and inhibitor complex structures of 4-oxalocrotonate tautomerase from Pseudomonas putida mt-2 (University of Texas at Austin-136 pages)
Authors: Taylor, A.B.
#1: Journal: Biochemistry / Year: 1998
Title: Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis
Authors: Taylor, A.B. / Czerwinski, R.M. / Johnson Jr., W.H. / Whitman, C.P. / Hackert, M.L.
History
DepositionOct 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE
G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
J: 4-OXALOCROTONATE TAUTOMERASE
K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)81,86212
Polymers81,86212
Non-polymers00
Water99155
1
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12410 Å2
ΔGint-68 kcal/mol
Surface area14180 Å2
MethodPISA, PQS
2
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE

C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE

C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12460 Å2
ΔGint-69 kcal/mol
Surface area14130 Å2
MethodPISA, PQS
3
E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE

E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE

E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12500 Å2
ΔGint-68 kcal/mol
Surface area14130 Å2
MethodPISA, PQS
4
G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE

G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE

G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12540 Å2
ΔGint-68 kcal/mol
Surface area14060 Å2
MethodPISA, PQS
5
I: 4-OXALOCROTONATE TAUTOMERASE
J: 4-OXALOCROTONATE TAUTOMERASE

I: 4-OXALOCROTONATE TAUTOMERASE
J: 4-OXALOCROTONATE TAUTOMERASE

I: 4-OXALOCROTONATE TAUTOMERASE
J: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12560 Å2
ΔGint-67 kcal/mol
Surface area14020 Å2
MethodPISA, PQS
6
K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE

K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE

K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12550 Å2
ΔGint-72 kcal/mol
Surface area13780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.400, 87.400, 254.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999992, -0.003782, -0.001351), (-0.003787, 0.999986, 0.003679), (0.001337, 0.003684, -0.999992)0.20839, -0.68188, 389.02017
2given(0.871607, 0.490203, -0.001478), (-0.490205, 0.871602, -0.00289), (-0.000129, 0.003243, 0.999995)0.39954, 0.49514, 38.49124
3given(-0.877978, 0.478459, 0.015253), (0.478657, 0.877884, 0.014367), (-0.006516, 0.019914, -0.999781)-2.86828, -2.65477, 427.56369
4given(-0.890159, -0.455648, 0.001407), (-0.45563, 0.890085, -0.012239), (0.004324, -0.011535, -0.999924)-0.32034, 2.27685, 350.16022
5given(0.891898, -0.451824, -0.019293), (0.452151, 0.891746, 0.018685), (0.008762, -0.025389, 0.999639)3.64598, -3.55254, -38.80231
6given(0.999766, 0.019, 0.010292), (-0.018948, 0.999808, -0.005037), (-0.010386, 0.004841, 0.999934)-1.92772, 1.00138, -132.39906
7given(-0.999819, -0.007238, -0.017606), (-0.007067, 0.999927, -0.009776), (0.017675, -0.00965, -0.999797)3.2762, 1.85401, 256.27512
8given(0.927262, 0.374076, 0.015897), (-0.373828, 0.927351, -0.016513), (-0.020919, 0.009369, 0.999737)-3.00616, 3.13832, -93.41225
9given(-0.932792, 0.360344, 0.007219), (0.360416, 0.932605, 0.018664), (-7.0E-6, 0.020011, -0.9998)-1.31933, -3.44844, 295.49902
10given(-0.913838, -0.406003, -0.00788), (-0.405801, 0.913759, -0.019246), (0.015014, -0.01439, -0.999784)1.36853, 3.66739, 217.45538
11given(0.92215, -0.386222, -0.021729), (0.386616, 0.922059, 0.018309), (0.012964, -0.025284, 0.999596)4.09595, -3.31456, -171.3802

-
Components

#1: Protein
4-OXALOCROTONATE TAUTOMERASE / 4-OXALOCROTONATE ISOMERASE


Mass: 6821.838 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: MT-2 / Plasmid: PBAOT1 / Gene (production host): XYLH / Production host: Escherichia coli (E. coli) / Strain (production host): S606
References: UniProt: Q01468, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.3 Å3/Da / Density % sol: 46 %
Description: PDB ENTRY 1OTF WAS USED TO SOLVE THE STARTING MOLECULAR REPLACEMENT MODEL
Crystal growpH: 7 / Details: pH 7.0

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 24488 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 19.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.168 / % possible all: 83.5

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SDMSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.3 ANGSTROMS RESOLUTION STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE FROM PSEUDOMONAS PUTIDA MT-2

Resolution: 2.5→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2405 9.8 %RANDOM
Rwork0.224 ---
obs0.224 24482 97.9 %-
Displacement parametersBiso mean: 45.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-15 Å
Luzzati sigma a0.45 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 0 55 5422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.58
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: RESTRAINTS
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 202 9.8 %
Rwork0.31 1864 -
obs--82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY

+
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://pdbjlvh1.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