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- PDB-5tvo: Crystal structure of Trypanosoma brucei AdoMetDC-delta26 monomer -

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Basic information

Entry
Database: PDB / ID: 5tvo
TitleCrystal structure of Trypanosoma brucei AdoMetDC-delta26 monomer
Components(S-adenosylmethionine decarboxylase proenzyme) x 2
KeywordsLYASE / autoinhibition / cis-proline
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / : / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 ...S-adenosylmethionine decarboxylase / : / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.481 Å
AuthorsVolkov, O.A. / Ariagno, C. / Chen, Z. / Tomchick, D.R. / Phillips, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R37AI034432 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI090599 United States
CitationJournal: Elife / Year: 2016
Title: Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog.
Authors: Volkov, O.A. / Kinch, L.N. / Ariagno, C. / Deng, X. / Zhong, S. / Grishin, N.V. / Tomchick, D.R. / Chen, Z. / Phillips, M.A.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine decarboxylase proenzyme
B: S-adenosylmethionine decarboxylase proenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8664
Polymers38,7552
Non-polymers1112
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-49 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.669, 75.644, 87.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S-adenosylmethionine decarboxylase proenzyme


Mass: 31971.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pET28bSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q587A7, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase proenzyme


Mass: 6782.649 Da / Num. of mol.: 1 / Fragment: UNP residues 27-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q587A7, adenosylmethionine decarboxylase
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H4O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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 Å3/Da / Density % sol: 38.45 % / Description: block
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % PEG 3350, 0.2 M Ammonium acetate, 0.1 M Bis-tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2015
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 51575 / % possible obs: 98.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.048 / Net I/σ(I): 29.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 4315 / CC1/2: 0.68 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EP9

3ep9


Resolution: 1.481→38.006 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 2000 3.89 %Random selection
Rwork0.1574 ---
obs0.159 51477 98.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.481→38.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 1 252 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152655
X-RAY DIFFRACTIONf_angle_d0.9873617
X-RAY DIFFRACTIONf_dihedral_angle_d17.297960
X-RAY DIFFRACTIONf_chiral_restr0.083396
X-RAY DIFFRACTIONf_plane_restr0.007459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4814-1.51850.35511150.26512855X-RAY DIFFRACTION81
1.5185-1.55950.27261350.21313327X-RAY DIFFRACTION93
1.5595-1.60540.25931430.19163537X-RAY DIFFRACTION100
1.6054-1.65730.23551440.17043541X-RAY DIFFRACTION100
1.6573-1.71650.27381440.15633577X-RAY DIFFRACTION100
1.7165-1.78520.18751440.14563567X-RAY DIFFRACTION100
1.7852-1.86650.22511450.14233572X-RAY DIFFRACTION100
1.8665-1.96490.22491440.14883564X-RAY DIFFRACTION100
1.9649-2.0880.18351440.1373577X-RAY DIFFRACTION100
2.088-2.24920.19841460.14223601X-RAY DIFFRACTION100
2.2492-2.47550.19191460.14723618X-RAY DIFFRACTION100
2.4755-2.83360.19621460.15943639X-RAY DIFFRACTION100
2.8336-3.56960.211500.15963688X-RAY DIFFRACTION100
3.5696-38.01880.16881540.15983814X-RAY DIFFRACTION100

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