[English] 日本語
Yorodumi
- PDB-3ep3: Human AdoMetDC D174N mutant with no putrescine bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ep3
TitleHuman AdoMetDC D174N mutant with no putrescine bound
Components
  • S-adenosylmethionine decarboxylase alpha chain
  • S-adenosylmethionine decarboxylase beta chain
KeywordsLYASE / AdoMetDC with mutation in putrescine binding site / Decarboxylase / Pyruvate / S-adenosyl-L-methionine / Spermidine biosynthesis / Zymogen
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 ...S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsBale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Basis for Putrescine Activation of Human S-Adenosylmethionine Decarboxylase.
Authors: Bale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: S-adenosylmethionine decarboxylase beta chain
A: S-adenosylmethionine decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7924
Polymers37,5822
Non-polymers2102
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-36 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.598, 55.240, 74.224
Angle α, β, γ (deg.)90.000, 109.640, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein S-adenosylmethionine decarboxylase beta chain / AdoMetDC / SamDC


Mass: 7694.577 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase alpha chain / AdoMetDC / SamDC


Mass: 29887.234 Da / Num. of mol.: 1 / Fragment: UNP residues 69-328 / Mutation: D174N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17707, adenosylmethionine decarboxylase
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 27642 / Num. obs: 26141 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 1.421 / Net I/σ(I): 15.869
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2187 / Rsym value: 0.39 / Χ2: 0.812 / % possible all: 73.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I7B

1i7b


Resolution: 1.84→34.95 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 519364 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1276 4.9 %RANDOM
Rwork0.243 ---
all0.243 27642 --
obs0.243 26141 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.163 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 95.97 Å2 / Biso mean: 46.261 Å2 / Biso min: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å20 Å2-2.76 Å2
2--16.6 Å20 Å2
3----12.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.84→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 13 179 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 144 4.7 %
Rwork0.335 2949 -
all-3093 -
obs-2187 61.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2pyruvoyl.parampyruvoyl.top
X-RAY DIFFRACTION3Tris.paramTris.top
X-RAY DIFFRACTION4water.param

+
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