[English] 日本語
Yorodumi
- PDB-4zgy: STRUCTURE of HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zgy
TitleSTRUCTURE of HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME
Components
  • Ornithine decarboxylase antizyme 1
  • Ornithine decarboxylase
KeywordsLYASE/LYASE INHIBITOR / TIM-BARREL DOMAIN / BETA-SHEET DOMAIN / DECARBOXYLATION / ANTIZYME / PLASMA / LYASE-LYASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of polyamine transmembrane transport / putrescine biosynthetic process from ornithine / ornithine decarboxylase / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process ...negative regulation of polyamine transmembrane transport / putrescine biosynthetic process from ornithine / ornithine decarboxylase / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / ornithine decarboxylase inhibitor activity / kidney development / response to virus / positive regulation of protein catabolic process / cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase - #60 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. ...Aminopeptidase - #60 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Acyl-CoA N-acyltransferase / Aminopeptidase / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Ornithine decarboxylase / Ornithine decarboxylase antizyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsWu, H.Y. / Chan, N.L.
Funding support Taiwan, 5items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNSC99-2113-M-002-008-MY3 Taiwan
Ministry of Science and TechnologyNSC101-2911-I-002-303- Taiwan
National Research Program for BiopharmaceuticalsNSC101-2325-B-002-049 Taiwan
National Taiwan UniversityNTU-102-027-MY3 Taiwan
National Taiwan UniversityNTU-103-008-MY3 Taiwan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis of antizyme-mediated regulation of polyamine homeostasis
Authors: Wu, H.Y. / Chen, S.F. / Hsieh, J.Y. / Chou, F. / Wang, Y.H. / Lin, W.T. / Lee, P.Y. / Yu, Y.J. / Lin, L.Y. / Lin, T.S. / Lin, C.L. / Liu, G.Y. / Tzeng, S.R. / Hung, H.C. / Chan, N.L.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_related / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine decarboxylase
B: Ornithine decarboxylase antizyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8194
Polymers62,5482
Non-polymers2712
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-25 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.698, 73.368, 162.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ornithine decarboxylase / / ODC


Mass: 46972.363 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ODC1 / Plasmid: 28A-ODC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P11926, ornithine decarboxylase
#2: Protein Ornithine decarboxylase antizyme 1 / / ODC-Az


Mass: 15575.625 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 95-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAZ1, OAZ / Plasmid: PQE30-AZ95 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P54368
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100MM MAGNESIUM ACETATE, 50MM MES PH 5.6, 20% 2-METHYL-2, 4-PENTANEDIOL(MPD), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
PH range: 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR(CRYSTAL TYPE SI(111))
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→24.3 Å / Num. obs: 17556 / % possible obs: 92.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 72.59 Å2 / Rsym value: 0.028 / Net I/σ(I): 23.9
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.76 / Rsym value: 0.193 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
PHENIX1.7.3_928refinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→24.29 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1753 10.01 %
Rwork0.203 --
obs0.208 17509 92.6 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.89 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 83.34 Å2
Baniso -1Baniso -2Baniso -3
1-17.4126 Å2-0 Å2-0 Å2
2---4.6616 Å20 Å2
3----10.2602 Å2
Refinement stepCycle: LAST / Resolution: 2.63→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 16 13 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034057
X-RAY DIFFRACTIONf_angle_d0.6785486
X-RAY DIFFRACTIONf_dihedral_angle_d10.981469
X-RAY DIFFRACTIONf_chiral_restr0.045614
X-RAY DIFFRACTIONf_plane_restr0.002699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6339-2.7050.38891230.30681104X-RAY DIFFRACTION86
2.705-2.78450.40371260.30521130X-RAY DIFFRACTION90
2.7845-2.87430.37551280.29341159X-RAY DIFFRACTION89
2.8743-2.97680.30641270.23841141X-RAY DIFFRACTION90
2.9768-3.09580.31061300.22511157X-RAY DIFFRACTION89
3.0958-3.23640.27711310.22771192X-RAY DIFFRACTION91
3.2364-3.40660.28891300.19811167X-RAY DIFFRACTION92
3.4066-3.61930.24191370.19651226X-RAY DIFFRACTION93
3.6193-3.89770.25021360.19291231X-RAY DIFFRACTION94
3.8977-4.28810.26141430.18031275X-RAY DIFFRACTION97
4.2881-4.90410.21831450.16731309X-RAY DIFFRACTION99
4.9041-6.16190.23031480.20771327X-RAY DIFFRACTION99
6.1619-24.29240.23891490.20491338X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 12.2419 Å / Origin y: 3.3242 Å / Origin z: 18.8422 Å
111213212223313233
T0.2573 Å20.0578 Å20.0092 Å2-0.4025 Å20.068 Å2--0.3154 Å2
L1.5258 °20.517 °2-0.632 °2-2.2021 °20.0999 °2--3.6546 °2
S0.0906 Å °0.0284 Å °-0.0639 Å °0.1017 Å °-0.2408 Å °0.0186 Å °0.1491 Å °0.4766 Å °0.1293 Å °
Refinement TLS groupSelection details: (chain 'A') or (chain 'B')

+
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