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- PDB-1vc3: Crystal Structure of L-Aspartate-alpha-Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 1vc3
TitleCrystal Structure of L-Aspartate-alpha-Decarboxylase
Components
  • L-Aspartate-alpha-Decarboxylase heavy chain
  • L-Aspartate-alpha-Decarboxylase light chain
KeywordsLYASE / Tetramer / pyruvoyl group / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNakajima, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of L-Aspartate-alpha-Decarboxylase
Authors: Goto, M. / Omi, R. / Nakajima, O. / Miyahara, I. / Hirotsu, K.
History
DepositionMar 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain


Theoretical massNumber of molelcules
Total (without water)13,1132
Polymers13,1132
Non-polymers00
Water2,846158
1
A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain

A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain


Theoretical massNumber of molelcules
Total (without water)26,2264
Polymers26,2264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+1,x-1,z1
2
A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain

A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain

A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain

A: L-Aspartate-alpha-Decarboxylase light chain
B: L-Aspartate-alpha-Decarboxylase heavy chain


Theoretical massNumber of molelcules
Total (without water)52,4528
Polymers52,4528
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area23620 Å2
ΔGint-121 kcal/mol
Surface area16100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.530, 67.530, 47.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein/peptide L-Aspartate-alpha-Decarboxylase light chain


Mass: 2817.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKN7, pyruvate decarboxylase
#2: Protein L-Aspartate-alpha-Decarboxylase heavy chain


Mass: 10295.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKN7*PLUS, pyruvate decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Potassium Sodium Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 16744 / % possible obs: 97.1 %
Reflection shellResolution: 1.04→1.08 Å / % possible all: 96.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 1702 10 %RANDOM
Rwork0.2151 ---
all-17252 --
obs-16653 --
Refine analyze
FreeObs
Luzzati coordinate error0.1 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 0 158 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.7

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