[English] 日本語
Yorodumi
- PDB-4ifk: Arginines 51 and 239* from a Neighboring Subunit are Essential fo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ifk
TitleArginines 51 and 239* from a Neighboring Subunit are Essential for Catalysis in a Zinc-dependent Decarboxylase
Components(2-amino-3-carboxymuconate 6-semialdehyde decarboxylase) x 2
KeywordsLYASE / TIM-BARREL / Decarboxylation / Metal-binding
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.012 Å
AuthorsHuo, L. / Davis, I. / Chen, L. / Liu, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase.
Authors: Huo, L. / Davis, I. / Chen, L. / Liu, A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_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_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.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.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_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: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6315
Polymers73,4762
Non-polymers1553
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-120 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.848, 49.062, 110.545
Angle α, β, γ (deg.)90.00, 127.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

-
Components

#1: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase


Mass: 36737.977 Da / Num. of mol.: 1 / Mutation: R239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V25
#2: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase


Mass: 36737.977 Da / Num. of mol.: 1 / Mutation: R51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V25
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.1 M Tris pH 8.75, 0.2 M MgCl2, 17% PEG5000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 43915 / Num. obs: 42861 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.107 / Χ2: 2.407 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.032.90.47819212.802187.6
2.03-2.073.20.42720191.74193
2.07-2.113.60.42821342.164196.6
2.11-2.154.10.43520751.703197.9
2.15-2.24.50.39621701.764198.3
2.2-2.254.90.37221031.375198
2.25-2.315.40.32821591.442198.4
2.31-2.375.90.31721211.378198.3
2.37-2.446.20.2921661.433198.6
2.44-2.526.60.25921461.651198.6
2.52-2.616.70.21821601.606198.8
2.61-2.7170.19221741.823198.8
2.71-2.847.20.1921672.318198.8
2.84-2.997.30.16921662.529199
2.99-3.177.50.14621732.678198.9
3.17-3.427.40.11221793.002199.1
3.42-3.767.10.08621993.483199.1
3.76-4.316.70.06721793.752199.1
4.31-5.426.50.05722223.768199
5.42-3560.05422283.965196.7

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HBV

2hbv


Resolution: 2.012→22.919 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.7995 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 2143 5.02 %Random
Rwork0.2088 ---
all0.2115 44084 --
obs0.2115 42682 96.82 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.756 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 93.96 Å2 / Biso mean: 39.6565 Å2 / Biso min: 14.76 Å2
Baniso -1Baniso -2Baniso -3
1--4.1293 Å20 Å2-0.855 Å2
2--13.7456 Å2-0 Å2
3----9.6163 Å2
Refinement stepCycle: LAST / Resolution: 2.012→22.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 3 229 5394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085312
X-RAY DIFFRACTIONf_angle_d1.1497199
X-RAY DIFFRACTIONf_chiral_restr0.082765
X-RAY DIFFRACTIONf_plane_restr0.005948
X-RAY DIFFRACTIONf_dihedral_angle_d14.6741940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0117-2.05850.32511260.24062237236381
2.0585-2.10990.29271280.23932591271994
2.1099-2.16690.28331200.23292722284297
2.1669-2.23060.28061340.22342729286398
2.2306-2.30260.29851580.22072691284998
2.3026-2.38480.25061500.21392673282398
2.3848-2.48010.27981330.22882755288898
2.4801-2.59290.25461420.22882749289198
2.5929-2.72940.27541490.21782734288398
2.7294-2.90010.28731460.22442748289498
2.9001-3.12350.29841380.23092735287399
3.1235-3.43690.25791430.20922772291599
3.4369-3.9320.25911510.19632768291999
3.932-4.94570.24511490.18552820296999
4.9457-22.92030.23911760.19322815299198

+
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