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- PDB-4aon: Conformational dynamics of aspartate alpha-decarboxylase active s... -

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Basic information

Entry
Database: PDB / ID: 4aon
TitleConformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl-L-aspartate complex
Components
  • ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
  • ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
KeywordsHYDROLASE / AMINO ACID METABOLISM / PROTEIN-DERIVED COFACTOR.
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytosol
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYorke, B.A. / Monteiro, D.C.F. / Pearson, A.R. / Webb, M.E.
CitationJournal: To be Published
Title: Conformational Dynamics of Aspartate Alpha Decarboxylase Active Site Revealed by Protein-Ligand Complexes
Authors: Yorke, B.A. / Monteiro, D.C.F. / Pearson, A.R. / Webb, M.E.
History
DepositionMar 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
B: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
D: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
E: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8566
Polymers31,5624
Non-polymers2942
Water3,657203
1
A: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
B: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
D: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
E: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
hetero molecules

A: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
B: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
D: ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN
E: ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,71212
Polymers63,1248
Non-polymers5894
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area24810 Å2
ΔGint-114.3 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.022, 71.022, 216.376
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-2006-

HOH

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Components

#1: Protein/peptide ASPARTATE-ALPHA-DECARBOXYLASE BETA CHAIN


Mass: 4770.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein ASPARTATE-ALPHA-DECARBOXYLASE ALPHA CHAIN


Mass: 11010.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: POSTTRANSLATIONAL MAIN CHAIN BREAK BETWEEN CHAIN A GLY24 AND CHAIN B SER25. SAME FOR CHAINS C AND D. SERINE 25 MODIFIED TO YIELD A PYRUVOYL COFACTOR IN BOTH CASES. IN THIS STRUCTURE THE ...Details: POSTTRANSLATIONAL MAIN CHAIN BREAK BETWEEN CHAIN A GLY24 AND CHAIN B SER25. SAME FOR CHAINS C AND D. SERINE 25 MODIFIED TO YIELD A PYRUVOYL COFACTOR IN BOTH CASES. IN THIS STRUCTURE THE BOUND LIGAND HAS FORMED A COVALENT IMINIUM INTERMEDIATE WITH PYR -25 IN BOTH SUBUNITS IN THE ASYMMETRIC UNIT
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: P0A790, aspartate 1-decarboxylase
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-GLUTAMATE (GLU): 1 NON-COVALENTLY BOUND L-GLUTAMATE MOLECULE IN EACH ADC ACTIVE SITE. PYRUVIC ...L-GLUTAMATE (GLU): 1 NON-COVALENTLY BOUND L-GLUTAMATE MOLECULE IN EACH ADC ACTIVE SITE. PYRUVIC ACID (PYR): POST-TRANSLATIONAL MODIFICATION OF RESIDUES 25 IN BOTH CHAINS B AND E TO EITHER PYRUVOYL GROUPS OR SERINE RESIDUES - 70:30 RATIO.
Sequence detailsHIS TAG PRESENT.

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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: 2.47 Å3/Da / Density % sol: 50.25 % / Description: NONE
Crystal growpH: 4.2
Details: 5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97779
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.5→59.16 Å / Num. obs: 52794 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 19 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AW8

1aw8


Resolution: 1.5→61.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.447 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.162 2682 5.1 %RANDOM
Rwork0.135 ---
obs0.136 49995 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å20 Å2
2---0.31 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.5→61.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 20 203 2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192012
X-RAY DIFFRACTIONr_bond_other_d0.0030.021348
X-RAY DIFFRACTIONr_angle_refined_deg2.511.9392736
X-RAY DIFFRACTIONr_angle_other_deg1.4723.0033281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36423.29997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2651519
X-RAY DIFFRACTIONr_chiral_restr0.1870.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022292
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02427
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.53533359
X-RAY DIFFRACTIONr_sphericity_free30.305551
X-RAY DIFFRACTIONr_sphericity_bonded13.00453469
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 178 -
Rwork0.196 3168 -
obs--96.8 %

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