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- PDB-1k0g: THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM PHOSP... -

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Basic information

Entry
Database: PDB / ID: 1k0g
TitleTHE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM PHOSPHATE 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
PHOSPHATE ION / TRYPTOPHAN / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)102,6436
Polymers102,0452
Non-polymers5984
Water10,088560
1
A: p-aminobenzoate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3223
Polymers51,0221
Non-polymers2992
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)51,3223
Polymers51,0221
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: p-aminobenzoate synthase component I
hetero molecules

B: p-aminobenzoate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6436
Polymers102,0452
Non-polymers5984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3840 Å2
ΔGint-31 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.010, 109.710, 134.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein p-aminobenzoate synthase component I / aminodeoxychorismate synthase component I / 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) / Gene: pabB / Plasmid: pKPabB / Production host: Escherichia coli (E. coli)
References: UniProt: P05041, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 3.43 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 1.6M Na/K Phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOL 0.1 M NA ...Details: 0.1M HEPES pH7.5, 1.6M Na/K Phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOL 0.1 M NA HEPES pH 7.5, 0.8 M NA PHOSPHATE, 0.8 M K PHOSPHATE)
Components of the solutions
IDNameCrystal-IDSol-ID
1MOPS pH 711
2KCL11
3MG CL211
4DTT11
5NA HEPES pH 7.512
6NA PHOSPHATE12
7K PHOSPHATE12
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 HEPES1reservoirpH7.5
70.8 Msodium phophate1reservoir
80.8 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0597 / Wavelength: 1.06 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.05971
21.061
ReflectionResolution: 2.05→20 Å / Num. all: 348268 / Num. obs: 88221 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 348268
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
MAR345data collection
X-GENdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PABB GROWN IN FORMATE, PDB ENTRY 1K0E

1k0e


Resolution: 2.05→10 Å / Num. parameters: 28923 / Num. restraintsaints: 27487 / 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
Rfree0.2376 4290 5.3 %RANDOM
all0.1725 81089 --
obs0.1726 -86.2 %-
Solvent computationSolvent model: METHOD USED : MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7227
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 40 560 7228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.057
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0226
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.091
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.023

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