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- PDB-2c45: NATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 2c45
TitleNATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE
ComponentsAspartate 1-decarboxylase
KeywordsLYASE / DOUBLE-PSI BETA BARREL / CARBOXYLASE / ZYMOGEN / PANTOTHENATE BIOSYNTHESIS / DECARBOXYLASE / PYRUVATE
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / peptidoglycan-based cell wall / 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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGopalan, G. / Chopra, S. / Ranganathan, A. / Swaminathan, K.
Citation
Journal: Proteins / Year: 2006
Title: Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis.
Authors: Gopalan, G. / Chopra, S. / Ranganathan, A. / Swaminathan, K.
#1: 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.
#2: 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. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the Schiff Base Intermediate Prior to Decarboxylation in the Catalytic Cycle of Aspartate Alpha-Decarboxylase
Authors: Lee, B.I. / Suh, S.W.
History
DepositionOct 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Aspartate 1-decarboxylase
D: Aspartate 1-decarboxylase
E: Aspartate 1-decarboxylase
F: Aspartate 1-decarboxylase
G: Aspartate 1-decarboxylase
H: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)119,2088
Polymers119,2088
Non-polymers00
Water88349
1
A: Aspartate 1-decarboxylase
B: Aspartate 1-decarboxylase
C: Aspartate 1-decarboxylase
D: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)59,6044
Polymers59,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Aspartate 1-decarboxylase
F: Aspartate 1-decarboxylase
G: Aspartate 1-decarboxylase
H: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)59,6044
Polymers59,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.100, 150.100, 60.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 14900.986 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.7 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SODIUM CACODYLATE (PH 6.5), 1.5 M MAGNESIUM SULPHATE AND 20% PEG2000, HANGING DROP, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 30363 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 1.1 Å2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 2.6 % / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPY

1ppy


Resolution: 2.99→7.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 105724.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE EIGHT MOLECULES IN THE ASYMMETRIC UNIT, FORMING TWO TETRAMERS. HEMIHEDRAL TWINNING WITH TWIN FRACTION 0.437 AND TWIN OPERATOR H,-H-K,-L. RESTRAINED NCS MODE WAS USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1959 8.6 %RANDOM
Rwork0.265 ---
obs0.265 22764 78.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9342 Å2 / ksol: 0.39434 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å26.82 Å20 Å2
2--2.31 Å20 Å2
3----4.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.99→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 0 49 6881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.99→3.12 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.317 118 8.9 %
Rwork0.282 1202 -
obs--36.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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