[English] 日本語
Yorodumi
- PDB-2ez2: Apo tyrosine phenol-lyase from Citrobacter freundii at pH 8.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ez2
TitleApo tyrosine phenol-lyase from Citrobacter freundii at pH 8.0
ComponentsTyrosine phenol-lyase
KeywordsLYASE / PLP-dependent enzyme / pyridoxal-5'-phosphate / domain closure
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
Similarity search - Function
Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMilic, D. / Matkovic-Calogovic, D. / Demidkina, T.V. / Antson, A.A.
CitationJournal: Biochemistry / Year: 2006
Title: Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions
Authors: Milic, D. / Matkovic-Calogovic, D. / Demidkina, T.V. / Kulikova, V.V. / Sinitzina, N.I. / Antson, A.A.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_conn.ptnr2_label_seq_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: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4026
Polymers103,1342
Non-polymers2684
Water18,3931021
1
A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules

A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,80312
Polymers206,2674
Non-polymers5368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area19490 Å2
ΔGint-114 kcal/mol
Surface area56220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.644, 143.735, 59.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2061-

HOH

21B-6039-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x, 143.735-y, z.

-
Components

#1: Protein Tyrosine phenol-lyase / E.C.4.1.99.2 / Beta-tyrosinase


Mass: 51566.785 Da / Num. of mol.: 2 / Fragment: Tyrosine phenol-lyase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: TPL / Plasmid: pTZTPL / Production host: Escherichia coli (E. coli) / Strain (production host): SVS370 / References: UniProt: P31013, tyrosine phenol-lyase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.8 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM potassium phosphate, 2 mM DDT, 0.2 M KCl, 32.5% (w/v) monomethyl ether PEG 2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 13, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→17 Å / Num. all: 95091 / Num. obs: 95091 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 / Χ2: 0.99
Reflection shellResolution: 1.85→1.88 Å / % possible obs: 85.1 % / Rmerge(I) obs: 0.381 / Num. measured obs: 4208 / Χ2: 0.946 / % possible all: 85.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→16.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.074 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 939 1 %RANDOM
Rwork0.174 ---
all0.175 93357 --
obs0.175 93357 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→16.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 12 1021 8257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227385
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9549950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87923.829363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.997151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791553
X-RAY DIFFRACTIONr_chiral_restr0.1070.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025635
X-RAY DIFFRACTIONr_nbd_refined0.2310.24168
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2911
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.248
X-RAY DIFFRACTIONr_mcbond_it1.3422.54514
X-RAY DIFFRACTIONr_mcangle_it2.14747236
X-RAY DIFFRACTIONr_scbond_it4.09262917
X-RAY DIFFRACTIONr_scangle_it5.907102714
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 65 -
Rwork0.222 5906 -
all-5971 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0758-0.05330.16691.3725-0.10981.13020.0623-0.14150.12850.292-0.0727-0.2935-0.20130.26090.01030.0351-0.1123-0.07240.00850.00430.026225.84493.98518.943
21.0086-0.5611-0.38131.32510.15470.95310.06490.0821-0.1089-0.11-0.0515-0.0850.15780.144-0.0134-0.01560.05780.0003-0.041-0.01-0.020117.69143.835-5.163
30.57340.3176-0.05621.2932-0.17260.5499-0.02960.055-0.0654-0.1607-0.0265-0.3141-0.05670.17920.0562-0.03-0.02060.04280.00140.02350.000627.39480.789-4.689
40.716-0.33180.00371.0469-0.18840.3364-0.0493-0.14570.01870.18480.0278-0.17830.06170.17530.0215-0.00580.049-0.05810.04580.0204-0.065224.47156.72720.702
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA19 - 4819 - 48
21AA333 - 456333 - 456
32BB19 - 4819 - 48
42BB333 - 456333 - 456
53AA57 - 31057 - 310
64BB57 - 31057 - 310

+
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