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- PDB-2nva: The X-ray crystal structure of the Paramecium bursaria Chlorella ... -

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Basic information

Entry
Database: PDB / ID: 2nva
TitleThe X-ray crystal structure of the Paramecium bursaria Chlorella virus arginine decarboxylase bound to agmatine
Componentsarginine decarboxylase, A207R protein
KeywordsLYASE / Arginine decarboxylase / PLP / TIM barrel / Eukaryotic ODC-like
Function / homology
Function and homology information


polyamine biosynthetic process / catalytic activity
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-PL2 / Arginine/Ornithine decarboxylase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShah, R.H. / Akella, R. / Goldsmith, E. / Phillips, M.A.
CitationJournal: Biochemistry / Year: 2007
Title: X-ray Structure of Paramecium bursaria Chlorella Virus Arginine Decarboxylase: Insight into the Structural Basis for Substrate Specificity.
Authors: Shah, R. / Akella, R. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionNov 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: 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: arginine decarboxylase, A207R protein
B: arginine decarboxylase, A207R protein
C: arginine decarboxylase, A207R protein
D: arginine decarboxylase, A207R protein
E: arginine decarboxylase, A207R protein
F: arginine decarboxylase, A207R protein
G: arginine decarboxylase, A207R protein
H: arginine decarboxylase, A207R protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,99516
Polymers336,1058
Non-polymers2,8918
Water26,4281467
1
A: arginine decarboxylase, A207R protein
B: arginine decarboxylase, A207R protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7494
Polymers84,0262
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-32 kcal/mol
Surface area26900 Å2
MethodPISA
2
C: arginine decarboxylase, A207R protein
D: arginine decarboxylase, A207R protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7494
Polymers84,0262
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-32 kcal/mol
Surface area27050 Å2
MethodPISA
3
E: arginine decarboxylase, A207R protein
F: arginine decarboxylase, A207R protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7494
Polymers84,0262
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-33 kcal/mol
Surface area27170 Å2
MethodPISA
4
G: arginine decarboxylase, A207R protein
H: arginine decarboxylase, A207R protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7494
Polymers84,0262
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-33 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.206, 117.275, 268.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological dimer is formed between Chains A and B, C and D, E and F, G and H in the asymmetric unit.

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Components

#1: Protein
arginine decarboxylase, A207R protein /


Mass: 42013.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Gene: A207R / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84527, arginine decarboxylase
#2: Chemical
ChemComp-PL2 / (4-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE


Mass: 361.334 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H24N5O5P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1467 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 6% PEG-8000, 100 mM imidazole, 200 mM calcium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2005 / Details: Mirrors
RadiationMonochromator: Double-crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 337817 / Num. obs: 337027 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.111 / Χ2: 0.907 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.249 / Num. unique all: 33474 / Χ2: 0.888 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NV9

2nv9


Resolution: 1.8→44.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.963 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2052 0.6 %RANDOM
Rwork0.219 ---
all0.2187 337027 --
obs0.219 336913 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23375 0 192 1467 25034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02224150
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.95332812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99952934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57624.5951147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.381153848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7341588
X-RAY DIFFRACTIONr_chiral_restr0.0910.23595
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218568
X-RAY DIFFRACTIONr_nbd_refined0.1920.212018
X-RAY DIFFRACTIONr_nbtor_refined0.3110.216880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.21588
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.231
X-RAY DIFFRACTIONr_mcbond_it0.4831.515081
X-RAY DIFFRACTIONr_mcangle_it0.574223903
X-RAY DIFFRACTIONr_scbond_it1.065310340
X-RAY DIFFRACTIONr_scangle_it1.4254.58909
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 165 -
Rwork0.261 24463 -
obs-24628 99.44 %

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