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- PDB-1n13: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylas... -

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Basic information

Entry
Database: PDB / ID: 1n13
TitleThe Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Components
  • Pyruvoyl-dependent arginine decarboxylase alpha chain
  • Pyruvoyl-dependent arginine decarboxylase beta chain
KeywordsLYASE / pyruvoyl group / pyruvate / arginine decarboxylase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionOct 16, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)108,08026
Polymers106,35312
Non-polymers1,72714
Water13,259736
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)54,04013
Polymers53,1776
Non-polymers8637
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21700 Å2
ΔGint-111 kcal/mol
Surface area18080 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)54,04013
Polymers53,1776
Non-polymers8637
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21530 Å2
ΔGint-109 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.460, 92.880, 87.110
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo (alpha beta)3 trimers are in the asymmetric unit.

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Components

#1: Protein
Pyruvoyl-dependent arginine decarboxylase beta chain / PvlArgDC


Mass: 5428.117 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-Codon-Plus(DE3)-RIL (Stratagene)
References: UniProt: Q57764, arginine decarboxylase
#2: Protein
Pyruvoyl-dependent arginine decarboxylase alpha chain / PvlArgDC


Mass: 12297.416 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-Codon-Plus(DE3)-RIL (Stratagene)
References: UniProt: Q57764, arginine decarboxylase
#3: Chemical
ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14N4
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.02 %
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, ...Details: PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta-octyl glucoside, putrescine, ethylenediaminetetraacetic acid, dithiothreitol, arginine methyl ester, 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.98
SYNCHROTRONAPS 8-BM20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 1, 2002
ADSC QUANTUM 3152CCDJan 1, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97931
ReflectionResolution: 1.4→29.16 Å / Num. all: 105327 / Num. obs: 103325 / % possible obs: 59.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.6 / Num. unique all: 771 / % possible all: 4.4
Reflection
*PLUS
Num. obs: 105327 / Num. measured all: 290225
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 0.044 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.16 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Model refined against first crystal (CHESS) data then later extended to higher resolution with inclusion of second data set (Rfree reflections kept consistent with addition of higher resolution data).
RfactorNum. reflection% reflectionSelection details
Rfree0.215 10235 10 %RANDOM
Rwork0.1915 ---
all0.196 105327 --
obs0.1915 101892 57.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1607 Å2 / ksol: 0.422321 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å20 Å2-0.99 Å2
2--6.79 Å20 Å2
3----2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 54 800 8260
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 181 10.7 %
Rwork0.231 1507 -
obs--5.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINAG2.PARAMPROTEINAG2.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD.PARAMMPD.TOP
Refinement
*PLUS
Highest resolution: 1.4 Å / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16
LS refinement shell
*PLUS
Lowest resolution: 1.45 Å / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.258

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