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- PDB-1k0e: THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM FORMA... -

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Basic information

Entry
Database: PDB / ID: 1k0e
TitleTHE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM FORMATE GROWN CRYSTALS
Componentsp-aminobenzoate synthase component I
KeywordsLYASE / AMINODEOXYCHORISMATE SYNTHASE / CHORISMATE / GLUTAMINE / TRYPTOPHAN / PABA SYNTHASE / P-AMINOBENZOATE SYNTHASE
Function / homology
Function and homology information


aminodeoxychorismate synthase complex / aminodeoxychorismate synthase / tryptophan binding / 4-amino-4-deoxychorismate synthase activity / 4-aminobenzoate biosynthetic process / L-tryptophan biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / protein heterodimerization activity / magnesium ion binding
Similarity search - Function
Aminodeoxychorismate synthase, component I / Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / TRYPTOPHAN / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsParsons, J.F. / Jensen, P.Y. / Pachikara, A.S. / Howard, A.J. / Eisenstein, E. / Ladner, J.E.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of Escherichia coli aminodeoxychorismate synthase: architectural conservation and diversity in chorismate-utilizing enzymes.
Authors: Parsons, J.F. / Jensen, P.Y. / Pachikara, A.S. / Howard, A.J. / Eisenstein, E. / Ladner, J.E.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p-aminobenzoate synthase component I
B: p-aminobenzoate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4995
Polymers102,0452
Non-polymers4543
Water5,729318
1
A: p-aminobenzoate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2733
Polymers51,0221
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: p-aminobenzoate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2272
Polymers51,0221
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.992, 185.718, 45.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein p-aminobenzoate synthase component I / aminodeoxychorismate synthase / ADC synthase


Mass: 51022.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pKPabB / Production host: Escherichia coli (E. coli)
References: UniProt: P05041, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate buffer, 2.0M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7.5, 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML ...Details: 0.1M sodium acetate buffer, 2.0M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7.5, 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOLUTION: 0.1 M NA ACETATE pH 4.6, 2.0 M NA FORMATE)
Components of the solutions
IDNameCrystal-IDSol-ID
1MOPS pH 7.511
2KCL11
3MG CL211
4DTT11
5NA ACETATE12
6NA FORMATE12
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140.2 mg/mlprotein1drop
250 mMMOPS1droppH7.4
350 mM1dropKCl
45 mM1dropMgCl2
52 mMdithiothreitol1drop
60.1 Msodium acetate1reservoirpH4.6
72.0 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2→20 Å / Num. all: 269253 / Num. obs: 55584 / % possible obs: 91.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.8 / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Redundancy: 5 % / Num. measured all: 269253 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 90.4 % / Redundancy: 3 %

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Processing

Software
NameClassification
SHELXDphasing
SHELXL-97refinement
MAR345data collection
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / Num. parameters: 28479 / Num. restraintsaints: 28146 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.3146 2896 5.2 %RANDOM
all0.2049 55584 --
obs0.206 -86.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7116
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6755 0 30 321 7106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.061
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0181
X-RAY DIFFRACTIONs_zero_chiral_vol0.017
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.086
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.205 / Rfactor Rfree: 0.315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.018

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