[English] 日本語
Yorodumi
- PDB-1mt1: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mt1
TitleThe Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii
Components
  • PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
  • PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
KeywordsLYASE / pyruvoyl group / pyruvate / agmatine / arginine
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / arginine catabolic process
Similarity search - Function
Pyruvoyl-dependent arginine decarboxylase / Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AGMATINE / Pyruvoyl-dependent arginine decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTolbert, W.D. / Graham, D.E. / White, R.H. / Ealick, S.E.
Citation
Journal: Structure / Year: 2003
Title: Pyruvoyl-Dependent Arginine Decarboxylase from Methanococcus jannaschii: Crystal Structures of the Self-Cleaved and S53A Proenzyme Forms
Authors: Tolbert, W.D. / Graham, D.E. / White, R.H. / Ealick, S.E.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis.
Authors: Graham, D.E. / Xu, H. / White, R.H.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Item: _software.classification / _software.name / _software.version
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl ...SEQUENCE Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl cofactor. RESIDUE 53 IS CONVERTED TO A PYRUVOYL GROUP.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
B: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
C: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
D: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
E: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
F: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
G: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
H: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
I: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
J: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
K: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
L: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69217
Polymers108,04112
Non-polymers6515
Water8,179454
1
A: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
B: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
C: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
D: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
E: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
F: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4119
Polymers54,0216
Non-polymers3913
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20460 Å2
ΔGint-127 kcal/mol
Surface area18420 Å2
MethodPISA
2
G: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
H: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
I: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
J: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
K: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
L: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2818
Polymers54,0216
Non-polymers2602
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-125 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.770, 92.990, 87.230
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo (alpha beta)3 trimers are located in the asymmetric unit. Each monomer undergoes an internal self cleavage reaction which generates a pyruvoyl cofactor.

-
Components

#1: Protein
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN


Mass: 5475.011 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0316 / Plasmid: pET19b (Novagen) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene)
References: UniProt: Q57764, arginine decarboxylase
#2: Protein
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN


Mass: 12531.892 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0316 / Plasmid: pET19b (Novagen) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene)
References: UniProt: Q57764, arginine decarboxylase
#3: Chemical
ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE / Agmatine


Mass: 130.191 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H14N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta octyl glucoside, putrescine, ethylenediaminetetraacetic acid dithiothreitol, pH 7. ...Details: PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta octyl glucoside, putrescine, ethylenediaminetetraacetic acid dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118-21 %PEG20001reservoir
210 %MPD1reservoir
32.5 %glycerol1reservoir
4100 mMHEPES1reservoirpH7.0
50.5 mMbeta-octylglucoside1reservoir
60.5 mMputrescine1reservoir
75 mMEDTA1reservoir
810 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.11→63.5 Å / Num. all: 57557 / Num. obs: 57557 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.142 / Net I/σ(I): 4.1
Reflection shellResolution: 2.11→2.24 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 8398 / Rsym value: 0.383 / % possible all: 100
Reflection
*PLUS
Num. obs: 52185 / % possible obs: 100 % / Num. measured all: 368924 / Rmerge(I) obs: 0.142
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.383

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SOLVEphasing
OASISmodel building
CNSrefinement
CCP4(SCALA)data scaling
OASISphasing
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 2.2→63.5 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Data was refined to the MLHL target in CNS. The number of reflections reported includes anomalous data.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 8839 9.8 %RANDOM
Rwork0.19 ---
all0.206 89997 --
obs0.19 89997 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4748 Å2 / ksol: 0.361126 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å20 Å2-1.43 Å2
2--9.83 Å20 Å2
3----5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7469 0 45 454 7968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.842
X-RAY DIFFRACTIONc_scangle_it4.182.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 1503 10 %
Rwork0.207 13547 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINAG2.PARAMPROTEINAG2.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.204

+
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