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- PDB-1et0: CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1et0
TitleCRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI
Components4-AMINO-4-DEOXYCHORISMATE LYASE
KeywordsLYASE / PSEUDO BETA BARREL
Function / homology
Function and homology information


aminodeoxychorismate lyase / 4-amino-4-deoxychorismate lyase activity / para-aminobenzoic acid biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aminodeoxychorismate lyase, class IV / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...Aminodeoxychorismate lyase, class IV / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aminodeoxychorismate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsNakai, T. / Mizutani, H. / Miyahara, I. / Hirotsu, K. / Takeda, S. / Jhee, K.H. / Yoshimura, T. / Esaki, N.
Citation
Journal: J.Biochem.(Tokyo) / Year: 2000
Title: Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli.
Authors: Nakai, T. / Mizutani, H. / Miyahara, I. / Hirotsu, K. / Takeda, S. / Jhee, K.H. / Yoshimura, T. / Esaki, N.
#1: Journal: J.Bacteriol. / Year: 1992
Title: Characterization and Sequence of Escherichia coli pabC, the Gene Encoding Aminodeoxychorismate Lyase, a Pyridoxal Phosphate-Containing Enzyme
Authors: Green, J.M. / Merkel, W.K. / Nichols, B.P.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-AMINO-4-DEOXYCHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9922
Polymers29,7451
Non-polymers2471
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 4-AMINO-4-DEOXYCHORISMATE LYASE
hetero molecules

A: 4-AMINO-4-DEOXYCHORISMATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9844
Polymers59,4902
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5420 Å2
ΔGint-26 kcal/mol
Surface area20430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.500, 73.930, 83.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein 4-AMINO-4-DEOXYCHORISMATE LYASE / ADC LYASE


Mass: 29745.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28305
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, 2-propanol, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.1 mMPLP1drop
320 mMpotassium phosphate1drop
417 %PEG60001reservoir
517 %2-propanol1reservoir
6100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 13365 / Num. obs: 12330 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.14 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 30.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.135 / Num. unique all: 1110 / % possible all: 85
Reflection
*PLUS
Num. measured all: 88073
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1210 -RANDOM
Rwork0.196 ---
all0.206 11997 --
obs0.204 11893 91.4 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 15 126 2088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.425

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