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- PDB-1uhd: Crystal structure of aspartate decarboxylase, pyruvoly group boun... -

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Basic information

Entry
Database: PDB / ID: 1uhd
TitleCrystal structure of aspartate decarboxylase, pyruvoly group bound form
Components
  • Aspartate 1-decarboxylase alpha chain
  • Aspartate 1-decarboxylase beta chain
KeywordsLYASE / double-psi beta barrel
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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLee, B.I. / Kwon, A.-R. / Han, B.W. / Suh, S.W.
CitationJournal: 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
DepositionJul 1, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 28, 2012Group: Non-polymer description
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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)13,3372
Polymers13,3372
Non-polymers00
Water28816
1
B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain

B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain

B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain

B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain


Theoretical massNumber of molelcules
Total (without water)53,3498
Polymers53,3498
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area23200 Å2
ΔGint-135 kcal/mol
Surface area18210 Å2
MethodPISA
2
B: Aspartate 1-decarboxylase beta chain
A: Aspartate 1-decarboxylase alpha chain
x 8


Theoretical massNumber of molelcules
Total (without water)106,69916
Polymers106,69916
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_575x,-y+2,-z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)81.875, 81.875, 93.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is tetramer from the monomer in the asymmetric unit by the operations: -y+1, x+1, z; -x, -y+2, z; y-1, -x+1,z

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Components

#1: Protein/peptide Aspartate 1-decarboxylase beta chain


Mass: 2806.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: PAND / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P56065, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase alpha chain


Mass: 10531.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: PAND / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P56065, aspartate 1-decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.96 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→34 Å / Num. obs: 11114 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.05
Reflection shellResolution: 2→2.11 Å / Redundancy: 10 % / Num. unique all: 1796 / Rsym value: 0.304 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1920909.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1145 10.3 %RANDOM
Rwork0.232 ---
obs0.232 11105 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7272 Å2 / ksol: 0.406518 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2--1.71 Å20 Å2
3----3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 16 949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
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→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 171 9.5 %
Rwork0.244 1625 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP_PVL.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3PROTEIN_REP_PVL.PARAM

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