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- PDB-4azd: T57V mutant of aspartate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 4azd
TitleT57V mutant of aspartate decarboxylase
ComponentsASPARTATE 1-DECARBOXYLASE
KeywordsLYASE / AMINO ACID SUBSTITUTION
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
MALONATE ION / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsWebb, M.E. / Yorke, B.A. / Kershaw, T. / Lovelock, S. / Lobley, C.M.C. / Kilkenny, M.L. / Smith, A.G. / Blundell, T.L. / Pearson, A.R. / Abell, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Threonine 57 is Required for the Post-Translational Activation of Escherichia Coli Aspartate Alpha-Decarboxylase
Authors: Webb, M.E. / Yorke, B.A. / Kershaw, T. / Lovelock, S. / Lobley, C.M.C. / Kilkenny, M.L. / Smith, A.G. / Blundell, T.L. / Pearson, A.R. / Abell, C.
History
DepositionJun 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: ASPARTATE 1-DECARBOXYLASE
B: ASPARTATE 1-DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9646
Polymers31,5562
Non-polymers4084
Water2,486138
1
A: ASPARTATE 1-DECARBOXYLASE
B: ASPARTATE 1-DECARBOXYLASE
hetero molecules

A: ASPARTATE 1-DECARBOXYLASE
B: ASPARTATE 1-DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,92812
Polymers63,1124
Non-polymers8168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area10320 Å2
ΔGint-9.1 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.920, 69.920, 217.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ASPARTATE 1-DECARBOXYLASE / L-ASPARTATE-ALPHA-DECARBOXYLASE / ASPARTATE ALPHA-DECARBOXYLASE / ASPARTATE 1-DECARBOXYLASE BETA ...L-ASPARTATE-ALPHA-DECARBOXYLASE / ASPARTATE ALPHA-DECARBOXYLASE / ASPARTATE 1-DECARBOXYLASE BETA CHAIN / ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN


Mass: 15777.928 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 57 TO VAL ENGINEERED RESIDUE IN CHAIN B, THR 57 TO VAL

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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: 2.44 Å3/Da / Density % sol: 49.56 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4 / Details: 2.4 M SODIUM MALONATE, 1.5 M (NH4)2SO4 PH 4, 292 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.62→26.46 Å / Num. obs: 38530 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPY

1ppy


Resolution: 1.62→26.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.204 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21709 1993 5 %RANDOM
Rwork0.18522 ---
obs0.18681 37850 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.128 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 28 138 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.9342622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05623.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54415315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2751518
X-RAY DIFFRACTIONr_chiral_restr0.2160.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021490
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5031.51209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39821935
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5033728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8724.5682
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.623→1.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 168 -
Rwork0.329 2768 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3048-0.10670.19940.2793-0.09630.5126-0.0126-0.0090.01660.01980.0115-0.0133-0.0253-0.01220.00110.00810.0008-0.00680.00650.00080.0066-6.0562-25.3985-6.3439
20.57-0.00640.2060.2787-0.01030.13170.00350.03050.0255-0.0345-0.0152-0.017-0.01390.02240.01180.0099-0.00180.00240.01450.00830.0057-4.3863-23.5628-28.3279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 117
2X-RAY DIFFRACTION2B1 - 117

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