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- PDB-1i2l: DEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1i2l
TitleDEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI WITH INHIBITOR
Components4-AMINO-4-DEOXYCHORISMATE LYASE
KeywordsLYASE / PYRIDOXAL PHOSPHATE / AMINODEOXYCHORISMATE / PABC / D-CYCLOSERINE
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
Chem-DCS / Aminodeoxychorismate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)30,0782
Polymers29,7451
Non-polymers3331
Water2,558142
1
A: 4-AMINO-4-DEOXYCHORISMATE LYASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,1574
Polymers59,4902
Non-polymers6662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5810 Å2
ΔGint-31 kcal/mol
Surface area20440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.494, 72.060, 81.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 37.01 %
Description: THE WATER MOLECULES HAVE BEEN ORDERED SO THAT THOSE THAT AGREE WITHIN 1.0 A OF WATER MOLECULES IN THE ADC LYASE 1.8 A STRUCTURE WITHOUT AN INHIBITOR ARE NUMBERED THE SAME. OTHER WATER ...Description: THE WATER MOLECULES HAVE BEEN ORDERED SO THAT THOSE THAT AGREE WITHIN 1.0 A OF WATER MOLECULES IN THE ADC LYASE 1.8 A STRUCTURE WITHOUT AN INHIBITOR ARE NUMBERED THE SAME. OTHER WATER MOLECULES ARE NUMBERED STARTING WITH 801.
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: 0.9879 / Wavelength: 0.9879 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98791
20.98791
ReflectionResolution: 2.3→36 Å / Num. obs: 10442 / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.7 / % possible all: 91.7

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ADC LYASE

Resolution: 2.3→36 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 542 5 %RANDOM
Rwork0.183 ---
obs-9900 95.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 22 142 2243

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