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- PDB-1pqf: Glycine 24 to Serine mutation of aspartate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 1pqf
TitleGlycine 24 to Serine mutation of aspartate decarboxylase
ComponentsAspartate 1-decarboxylase
KeywordsLYASE / pyruvoyl-dependent decarboxylase / intramolecular protein self-processing
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: 2 Å
AuthorsSchmitzberger, F. / Kilkenny, M.L. / Lobley, C.M.C. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.
Citation
Journal: Embo J. / Year: 2003
Title: Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase
Authors: Schmitzberger, F. / Kilkenny, M.L. / Lobley, C.M.C. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.
#1: Journal: J.Biol.Chem. / Year: 1979
Title: Purification and properties of L-Aspartate-alpha-decarboxylase, an enzyme that catalyzes the formation of beta-alanine in Escherichia coli
Authors: Williamson, J.M. / Brown, G.M.
#2: Journal: Biochem.J. / Year: 1997
Title: Escherichia coli L-aspartate-alpha-decarboxylase: preprotein processing and observation of reaction intermediates by electrospray mass spectrometry
Authors: Ramjee, M.K. / Genschel, U. / Abell, C. / Smith, A.G.
#3: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of aspartate decarboxylase at 2.2A resolution provides evidence for an ester in protein self-processing
Authors: Albert, A. / Dhanaraj, V. / Genschel, U. / Khan, G. / Ramjee, M.K. / Pulido, R. / Sibanda, B.L. / von Delft, F. / Witty, M. / Blundell, T.L. / Smith, A.G. / Abell, C.
History
DepositionJun 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,8444
Polymers31,6522
Non-polymers1922
Water4,252236
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)63,6888
Polymers63,3044
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area8150 Å2
ΔGint-110 kcal/mol
Surface area19590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.436, 71.436, 219.157
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-328-

HOH

DetailsThe asymmetric unit contains two protomers. The biological unit is a tetramer, which is created by the symmetry operator: x,x-y,1/6-z

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Components

#1: Protein Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase


Mass: 15825.926 Da / Num. of mol.: 2 / Mutation: G24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND / Plasmid: pRESTA / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: NH42SO4, citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-9 mg/mlprotein1drop
21.4-1.6 Mammonium sulfate1reservoir
30.1 Mcitric acid1reservoirpH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2002
RadiationMonochromator: slits / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 23414 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 30.9 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.078 / Net I/σ(I): 33.8
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.345 / % possible all: 90.5
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AW8

1aw8


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.587 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18464 1180 5.1 %RANDOM
Rwork0.16541 ---
all0.16636 23414 --
obs0.16636 21839 98.76 %-
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: 14.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.08 Å2
Refine analyzeLuzzati coordinate error free: 0.117 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 10 236 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211901
X-RAY DIFFRACTIONr_bond_other_d0.0020.021721
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9312579
X-RAY DIFFRACTIONr_angle_other_deg0.83333981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895241
X-RAY DIFFRACTIONr_chiral_restr0.0910.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022139
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02390
X-RAY DIFFRACTIONr_nbd_refined0.2190.2344
X-RAY DIFFRACTIONr_nbd_other0.2570.22073
X-RAY DIFFRACTIONr_nbtor_other0.1060.21218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.237
X-RAY DIFFRACTIONr_mcbond_it0.6731.51208
X-RAY DIFFRACTIONr_mcangle_it1.26921933
X-RAY DIFFRACTIONr_scbond_it2.2423693
X-RAY DIFFRACTIONr_scangle_it3.7084.5646
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 92
Rwork0.187 1423
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)
143.96316.438-2.485355.05529.636414.17420.079-0.2103-1.6552.697-0.25172.76581.5378-2.1120.17260.3492-0.13890.00520.44560.02680.308341.086829.737110.8968
25.90933.85556.21373.56976.00188.8773-0.176-0.13630.1841-0.18390.0781-0.0059-0.39940.1020.0980.0782-0.0453-0.02270.05890.03960.02855.826346.250327.7491
363.5659-31.11534.013620.9868-7.93615.2679-1.6508-3.355-0.53062.19341.0131-0.7387-0.059-0.02860.63780.3740.065-0.16360.30580.00290.217867.439437.782139.2258
41.16321.50621.2452.31451.81732.8132-0.0819-0.0040.0456-0.02080.0517-0.0874-0.08590.07050.03020.0669-0.0006-0.01060.06330.01280.050356.119245.236330.9669
53.53918.81311.670335.05336.22297.17230.2831-1.1311-0.2661-1.7951-0.90890.2324-0.44860.63170.62580.46430.0602-0.00490.42030.01110.405550.132561.243730.5467
62.27571.0352-0.17349.5013-1.5073.25440.11710.08820.2711-0.2884-0.2403-0.4744-0.3960.28250.12320.0518-0.02450.0050.09360.040.086856.808442.34916.4545
717.74147.4269-4.160811.38052.693234.55250.1178-0.96211.51160.729-1.27970.1903-2.4362-0.5851.16190.4531-0.0315-0.15460.18050.00950.241657.033956.593218.7217
811.12062.76175.69435.8885-4.53721.54130.0975-0.04470.3859-0.0771-0.5607-0.2281-0.42180.35360.46320.2208-0.03960.01990.05220.03060.105651.904353.31398.3398
91.79570.3944-0.03864.6296-0.12742.21840.05750.13790.2155-0.2238-0.0747-0.4311-0.43440.32910.01720.118-0.04220.0040.12020.05160.09855.495746.43926.7409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-3 - 114 - 18
2X-RAY DIFFRACTION2AA2 - 1919 - 36
3X-RAY DIFFRACTION3AA20 - 2637 - 43
4X-RAY DIFFRACTION4AA27 - 11544 - 132
5X-RAY DIFFRACTION5AA116 - 123133 - 140
6X-RAY DIFFRACTION6BB1 - 1918 - 36
7X-RAY DIFFRACTION7BB20 - 2637 - 43
8X-RAY DIFFRACTION8BB27 - 2944 - 46
9X-RAY DIFFRACTION9BB30 - 11647 - 133
Refinement
*PLUS
Rfactor Rfree: 0.182 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.57
LS refinement shell
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.185

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