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- PDB-2qqc: E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Me... -

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Basic information

Entry
Database: PDB / ID: 2qqc
TitleE109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Components
  • Pyruvoyl-dependent arginine decarboxylase subunit alpha
  • Pyruvoyl-dependent arginine decarboxylase subunit beta
KeywordsLYASE / arginine decarboxylase / pyruvoyl / decarboxylation / autoprocessing / serinolysis / Pyruvate
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: 2 Å
AuthorsEalick, S.E. / Soriano, E.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.
Authors: Soriano, E.V. / McCloskey, D.E. / Kinsland, C. / Pegg, A.E. / Ealick, S.E.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 2.0Aug 30, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.0Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvoyl-dependent arginine decarboxylase subunit beta
B: Pyruvoyl-dependent arginine decarboxylase subunit alpha
C: Pyruvoyl-dependent arginine decarboxylase subunit beta
D: Pyruvoyl-dependent arginine decarboxylase subunit alpha
E: Pyruvoyl-dependent arginine decarboxylase subunit beta
F: Pyruvoyl-dependent arginine decarboxylase subunit alpha
G: Pyruvoyl-dependent arginine decarboxylase subunit beta
H: Pyruvoyl-dependent arginine decarboxylase subunit alpha
I: Pyruvoyl-dependent arginine decarboxylase subunit beta
J: Pyruvoyl-dependent arginine decarboxylase subunit alpha
K: Pyruvoyl-dependent arginine decarboxylase subunit beta
L: Pyruvoyl-dependent arginine decarboxylase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,43022
Polymers107,17612
Non-polymers1,25410
Water9,026501
1
A: Pyruvoyl-dependent arginine decarboxylase subunit beta
B: Pyruvoyl-dependent arginine decarboxylase subunit alpha
C: Pyruvoyl-dependent arginine decarboxylase subunit beta
D: Pyruvoyl-dependent arginine decarboxylase subunit alpha
E: Pyruvoyl-dependent arginine decarboxylase subunit beta
F: Pyruvoyl-dependent arginine decarboxylase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,33312
Polymers53,5886
Non-polymers7456
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21440 Å2
MethodPISA
2
G: Pyruvoyl-dependent arginine decarboxylase subunit beta
H: Pyruvoyl-dependent arginine decarboxylase subunit alpha
I: Pyruvoyl-dependent arginine decarboxylase subunit beta
J: Pyruvoyl-dependent arginine decarboxylase subunit alpha
K: Pyruvoyl-dependent arginine decarboxylase subunit beta
L: Pyruvoyl-dependent arginine decarboxylase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,09710
Polymers53,5886
Non-polymers5094
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.108, 92.810, 85.707
Angle α, β, γ (deg.)90.00, 95.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvoyl-dependent arginine decarboxylase subunit beta


Mass: 5566.263 Da / Num. of mol.: 6 / Fragment: Beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pdaD, MJ0316 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57764
#2: Protein
Pyruvoyl-dependent arginine decarboxylase subunit alpha


Mass: 12296.432 Da / Num. of mol.: 6 / Fragment: Alpha subunit / Mutation: E109Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pdaD, MJ0316 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57764
#3: Chemical
ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE / Agmatine


Mass: 130.191 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14N4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17-20% PEG 2000, 10% MPD, 2.5% glycerol, 0.1 M HEPES, 0.005 M beta-octylglucoside, 0.005 M EDTA, 0.010 M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→46.13 Å / Num. all: 60058 / Num. obs: 59694 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.4 % / Rsym value: 0.135 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N13

1n13


Resolution: 2→44.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 350977.98 / 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
Rfree0.237 6043 10.1 %RANDOM
Rwork0.194 ---
all0.194 60058 --
obs0.194 59694 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8874 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.41 Å2
2--5.9 Å20 Å2
3----6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 84 533 7630
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
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 973 10.1 %
Rwork0.189 8633 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3pyru.parampyru.top
X-RAY DIFFRACTION4ag.paramag.top
X-RAY DIFFRACTION5MPD.paramMPD.top

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