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- PDB-1i2k: AMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1i2k
TitleAMINODEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI
Components4-AMINO-4-DEOXYCHORISMATE LYASE
KeywordsLYASE / PYRIDOXAL PHOSPHATE / AMINODEOXYCHORISMATE / PABC
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 / AB INITIO / Resolution: 1.79 Å
AuthorsJensen, P.Y. / Parsons, J.F. / Fisher, K.E. / Pachikara, A.S. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Ladner, J.E.
CitationJournal: To be Published
Title: Structure and Mechanism of Escherichia coli Aminodeoxychorismate Lyase
Authors: Jensen, P.Y. / Parsons, J.F. / Fisher, K.E. / Pachikara, A.S. / Tordova, M. / Howard, A.J. / Eisenstein, E. / Ladner, J.E.
History
DepositionFeb 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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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
Water3,819212
1
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_655-x+1,-y,z1
Buried area5610 Å2
ΔGint-29 kcal/mol
Surface area21050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.047, 72.966, 82.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

DetailsThe second chain in the dimer is generated by the crystal two fold: Use the symmetry -x,-y,z and add one cell in X

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Components

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


Mass: 29745.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PABC / Production host: Escherichia coli (E. coli) / References: UniProt: P28305, Lyases
#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.: 212 / 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 Å3/Da / Density % sol: 39.54 %
Description: THE WATER MOLECULES HAVE BEEN ORDERED SO THAT THE FIRST 177 FORM THE FIRST HYDRATION SPHERE, THE NEXT 30 BELONG TO THE SECOND HYDRATION SHPERE AND THE FINAL 5 BELONG TO THE THIRD HYDRATION SHPERE.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 0.2M magnesium acetate, 0.1M HEPES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: BRUKER / Detector: CCD / Date: Jul 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→36 Å / Num. obs: 21637 / % possible obs: 92.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.8 / % possible all: 88.3

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.79→10 Å / Num. parameters: 9409 / Num. restraintsaints: 8766 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.248 115 5 %RANDOM
Rwork0.1641 ---
all0.163 21637 --
obs0.164 -93.1 %-
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2305.5
Refinement stepCycle: LAST / Resolution: 1.79→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 15 212 2306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0271
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.079
X-RAY DIFFRACTIONs_approx_iso_adps0

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