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- PDB-1pt0: Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Al... -

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Basic information

Entry
Database: PDB / ID: 1pt0
TitleUnprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26
ComponentsAspartate 1-decarboxylase
KeywordsLYASE / Decarboxylase / Pantothenate pathway / 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 2.2 A 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 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / 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
B: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7983
Polymers31,7022
Non-polymers961
Water3,153175
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)63,5966
Polymers63,4044
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area7700 Å2
ΔGint-77 kcal/mol
Surface area17720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.935, 70.935, 217.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological unit is a tetramer generated from the symmetry operator x,x-y+1,1/6-z

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Components

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


Mass: 15850.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND / Plasmid: pRSETa / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.4-1.6M Ammonium Sulphate, 0.1M Citric Acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
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: slit / 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. all: 23013 / Num. obs: 22903 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 23.7 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 37.54
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 256.6 / Rsym value: 0.1071 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Num. obs: 23013 / Redundancy: 28.7 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.3 % / Mean I/σ(I) obs: 10.7

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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→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.596 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19084 1669 7.3 %RANDOM
Rwork0.17394 ---
all0.17519 23013 --
obs0.17519 21139 99.62 %-
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: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refine analyzeLuzzati coordinate error free: 0.118 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 5 175 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211787
X-RAY DIFFRACTIONr_bond_other_d0.0030.021603
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9142425
X-RAY DIFFRACTIONr_angle_other_deg1.10633693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2015233
X-RAY DIFFRACTIONr_chiral_restr0.1350.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022047
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02374
X-RAY DIFFRACTIONr_nbd_refined0.2030.2336
X-RAY DIFFRACTIONr_nbd_other0.2570.21936
X-RAY DIFFRACTIONr_nbtor_other0.0860.21071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.221
X-RAY DIFFRACTIONr_mcbond_it0.7311.51153
X-RAY DIFFRACTIONr_mcangle_it1.34921834
X-RAY DIFFRACTIONr_scbond_it2.2833634
X-RAY DIFFRACTIONr_scangle_it3.8354.5590
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.201 126
Rwork0.182 1483
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)
15.1281.50513.76062.69793.46486.586-0.2047-0.04050.3451-0.3406-0.05590.1633-0.5194-0.01410.26050.1295-0.0201-0.00910.05440.06780.0867264.6966-78.452923.5882
226.6681-9.4941-9.199626.792411.05819.33220.0147-0.5488-0.71931.09520.4104-1.38771.19710.9132-0.42510.1855-0.0138-0.13910.2311-0.03580.2137280.0461-77.065540.005
362.4781-9.344713.21927.6637-5.18034.10860.2153-1.0792-0.95850.7479-0.1389-1.47230.22990.9376-0.07640.34570.0053-0.15450.5085-0.08220.4335283.0165-83.968237.6862
41.19631.31321.39721.75211.51392.6926-0.0278-0.05290.08660.0152-0.004-0.0197-0.11160.0220.03180.1293-0.0091-0.0150.13550.00710.1174268.1201-78.126930.7961
52.42140.4284-0.06249.1238-0.90233.62580.05020.21070.1364-0.6768-0.1008-0.4878-0.10680.21240.05060.07640.00640.02440.15350.04220.0939268.4775-84.6485.4568
667.304610.197761.589940.669128.470784.2059-0.58-2.91250.68151.31420.9996-1.2292-1.7568-1.6848-0.41960.4507-0.03390.11630.3707-0.02650.5146273.4314-63.558812.1348
718.598112.889629.028348.575232.306983.70240.2176-2.01030.90682.3233-0.0376-1.9792-1.6521-0.656-0.180.3653-0.0624-0.06980.3887-0.09220.4968270.2242-67.401619.4979
82.7770.0462-0.57943.5077-0.31512.01310.12020.15980.4805-0.2127-0.0162-0.2685-0.4960.1432-0.10390.2059-0.02560.02140.14920.05910.1687267.7077-76.98887.1609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1517 - 32
2X-RAY DIFFRACTION2AA16 - 1933 - 36
3X-RAY DIFFRACTION3AA20 - 2737 - 44
4X-RAY DIFFRACTION4AA28 - 11645 - 133
5X-RAY DIFFRACTION5BB1 - 1518 - 32
6X-RAY DIFFRACTION6BB16 - 2033 - 37
7X-RAY DIFFRACTION7BB21 - 2738 - 44
8X-RAY DIFFRACTION8BB28 - 11645 - 133
Refinement
*PLUS
Num. reflection Rfree: 69 / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.59
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.172

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