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- PDB-3tm7: Processed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala -

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Basic information

Entry
Database: PDB / ID: 3tm7
TitleProcessed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala
Components
  • Aspartate 1-decarboxylase alpha chain
  • Aspartate 1-decarboxylase beta chain
KeywordsLYASE / AUTO-PROCESSING / Pyruvoyl
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
Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWebb, M.E. / Lobley, C.M.C. / Soliman, F. / Kilkenny, M.L. / Smith, A.G. / Abell, C. / Blundell, T.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Escherichia coli aspartate alpha-decarboxylase Asn72Ala: probing the role of Asn72 in pyruvoyl cofactor formation
Authors: Webb, M.E. / Lobley, C.M. / Soliman, F. / Kilkenny, M.L. / Smith, A.G. / Blundell, T.L. / Abell, C.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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 beta chain
B: Aspartate 1-decarboxylase alpha chain
C: Aspartate 1-decarboxylase beta chain
D: Aspartate 1-decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1326
Polymers27,9404
Non-polymers1922
Water4,089227
1
A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
C: Aspartate 1-decarboxylase beta chain
D: Aspartate 1-decarboxylase alpha chain
hetero molecules

A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
C: Aspartate 1-decarboxylase beta chain
D: Aspartate 1-decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26412
Polymers55,8798
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area22440 Å2
ΔGint-215 kcal/mol
Surface area18950 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.083, 71.083, 215.807
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/peptide Aspartate 1-decarboxylase beta chain / Aspartate alpha-decarboxylase


Mass: 2985.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0131, JW0127, panD / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase alpha chain / Aspartate alpha-decarboxylase


Mass: 10984.321 Da / Num. of mol.: 2 / Mutation: N72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0131, JW0127, panD / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.6-2.4M ammonium sulphate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9781 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 7, 2003
RadiationMonochromator: horizontally focusing optimized for 1.488 and 0.98A
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 36655 / Num. obs: 36655 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.75 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 59.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 11.75 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 9.3 / Num. unique all: 36655 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.202 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18409 1826 5 %RANDOM
Rwork0.16024 ---
all0.16142 34687 --
obs0.16142 34687 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 10 227 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211904
X-RAY DIFFRACTIONr_bond_other_d0.0020.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9242581
X-RAY DIFFRACTIONr_angle_other_deg1.07234070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8145241
X-RAY DIFFRACTIONr_chiral_restr0.1790.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022125
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02390
X-RAY DIFFRACTIONr_nbd_refined0.230.2353
X-RAY DIFFRACTIONr_nbd_other0.2530.22130
X-RAY DIFFRACTIONr_nbtor_other0.0850.21209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3130.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3410.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4680.238
X-RAY DIFFRACTIONr_mcbond_it2.16551216
X-RAY DIFFRACTIONr_mcangle_it3.30261942
X-RAY DIFFRACTIONr_scbond_it3.7985688
X-RAY DIFFRACTIONr_scangle_it5.5427.5639
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.173 125
Rwork0.161 2507

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