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- PDB-2ejb: Crystal Structure Of Phenylacrylic Acid Decarboxylase from Aquife... -

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Basic information

Entry
Database: PDB / ID: 2ejb
TitleCrystal Structure Of Phenylacrylic Acid Decarboxylase from Aquifex aeolicus
ComponentsProbable aromatic acid decarboxylase
KeywordsLYASE / Phenylacrylic Acid Decarboxylase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Phenylacrylic Acid Decarboxylase from Aquifex aeolicus
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionMar 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: Probable aromatic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)21,2861
Polymers21,2861
Non-polymers00
Water1,42379
1
A: Probable aromatic acid decarboxylase

A: Probable aromatic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,5722
Polymers42,5722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
Buried area3250 Å2
ΔGint-23.9 kcal/mol
Surface area15880 Å2
MethodPISA
2
A: Probable aromatic acid decarboxylase
x 12


Theoretical massNumber of molelcules
Total (without water)255,43112
Polymers255,43112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation38_555-x+1/2,-y+1/2,z1
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
Buried area42150 Å2
ΔGint-127.8 kcal/mol
Surface area72620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.934, 130.934, 130.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21A-234-

HOH

31A-250-

HOH

41A-259-

HOH

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Components

#1: Protein Probable aromatic acid decarboxylase / phenylacrylic acid decarboxylase


Mass: 21285.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL
References: UniProt: O66811, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.5
Details: 10% PEG 6000, 2M NaCl, pH 4.5, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→32.73 Å / Num. all: 10214 / Num. obs: 9696 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.038 / Net I/σ(I): 36.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.8 / Num. unique all: 954 / Rsym value: 0.294 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SBZ

1sbz


Resolution: 2.15→32.73 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 493 -RANDOM
Rwork0.217 ---
obs0.217 9696 94.9 %-
all-10214 --
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.15→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 0 79 1452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.283 57 -
Rwork0.249 --
obs-966 95.5 %

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