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- PDB-1n2m: The S53A Proenzyme Structure of Methanococcus jannaschii. -

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Basic information

Entry
Database: PDB / ID: 1n2m
TitleThe S53A Proenzyme Structure of Methanococcus jannaschii.
ComponentsPyruvoyl-dependent arginine decarboxylase
KeywordsLYASE / pyruvoyl group / pyruvate / agmatine / arginine decarboxylase
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / L-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 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyruvoyl-dependent arginine decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 23, 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 1.3Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Pyruvoyl-dependent arginine decarboxylase
B: Pyruvoyl-dependent arginine decarboxylase
C: Pyruvoyl-dependent arginine decarboxylase
D: Pyruvoyl-dependent arginine decarboxylase
E: Pyruvoyl-dependent arginine decarboxylase
F: Pyruvoyl-dependent arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,19714
Polymers106,2516
Non-polymers9458
Water8,971498
1
A: Pyruvoyl-dependent arginine decarboxylase
B: Pyruvoyl-dependent arginine decarboxylase
C: Pyruvoyl-dependent arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5987
Polymers53,1263
Non-polymers4734
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-48 kcal/mol
Surface area18540 Å2
MethodPISA
2
D: Pyruvoyl-dependent arginine decarboxylase
E: Pyruvoyl-dependent arginine decarboxylase
F: Pyruvoyl-dependent arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5987
Polymers53,1263
Non-polymers4734
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-43 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.260, 91.310, 86.200
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo proenzyme trimers are in the asymmetric unit.

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Components

#1: Protein
Pyruvoyl-dependent arginine decarboxylase / PvlArgDC


Mass: 17708.564 Da / Num. of mol.: 6 / Mutation: S53A
Source method: isolated from a genetically manipulated source
Details: proenzyme form
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.36 %
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-ethansulfonic 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-ethansulfonic 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.947 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2002
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.9→28.7 Å / Num. all: 68424 / Num. obs: 61718 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.85 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 3497 / Rsym value: 0.262 / % possible all: 51.5
Reflection
*PLUS
Num. measured all: 187377 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 51.5 % / Rmerge(I) obs: 0.262

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MT1

1mt1


Resolution: 1.9→28.69 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5966 10 %RANDOM
Rwork0.186 ---
all0.203 68392 --
obs0.186 59911 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.2446 Å2 / ksol: 0.413056 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å20 Å20.35 Å2
2--12.54 Å20 Å2
3----7.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7275 0 0 562 7837
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 565 9.4 %
Rwork0.228 5440 -
obs--52.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINMAO.PARAMPROTEINMAO.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD.PARAMMPD.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.233

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