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- PDB-1mt1: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylas... -

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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 / 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 / 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
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)108,69217
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.

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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


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


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 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

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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

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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

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