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- PDB-5e2l: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 5e2l
Title3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D-phenylalanine
Components3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
KeywordsTRANSFERASE / 3-Deoxy-7-Phosphoheptulosonate Synthase / allosteric regulation / allosteric site / amino acid
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
D-PHENYLALANINE / : / Phospho-2-dehydro-3-deoxyheptonate aldolase / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReichau, S. / Jiao, W. / Parker, E.J.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
New Zealand Marsden FundUOC1105 New Zealand
Maurice Wilkins Centre for Molecular Biodiscovery New Zealand
CitationJournal: Plos One / Year: 2016
Title: Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using -Amino Acids.
Authors: Reichau, S. / Blackmore, N.J. / Jiao, W. / Parker, E.J.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_reflns_twin / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,93918
Polymers101,6572
Non-polymers1,28216
Water1,47782
1
A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules

A: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,87836
Polymers203,3144
Non-polymers2,56432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area16890 Å2
ΔGint-352 kcal/mol
Surface area65390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.989, 203.989, 66.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21B-608-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase


Mass: 50828.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E8NFD1, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 6 types, 98 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DPN / D-PHENYLALANINE / Phenylalanine


Type: D-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.95 Å3/Da / Density % sol: 68.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M TRIS-HCl, pH 7.5, 1.5M ammonium sulfate, 12% v/v glycerol. Crystals were soaked in the same solution with an additional 10% v/v glycerol and 2.5 mM D-phenylalanine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 26, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.579
11-h,-k,l20.421
ReflectionResolution: 2.5→49 Å / Num. obs: 55365 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.059 / Net I/σ(I): 12 / Num. measured all: 620384
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.5-2.5711.50.8535191845290.770.262100
10.61-499.80.0528.876467800.9990.01799

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NV8

3nv8


Resolution: 2.5→49 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1462 / WRfactor Rwork: 0.131 / FOM work R set: 0.8967 / SU B: 7.197 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0465 / SU Rfree: 0.0347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 2718 4.9 %RANDOM
Rwork0.1557 ---
obs0.1566 52625 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.88 Å2 / Biso mean: 35.628 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å20 Å2
2--2.93 Å20 Å2
3----5.86 Å2
Refinement stepCycle: final / Resolution: 2.5→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7046 0 63 82 7191
Biso mean--36.13 30.23 -
Num. residues----921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197296
X-RAY DIFFRACTIONr_bond_other_d0.0010.026935
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9679934
X-RAY DIFFRACTIONr_angle_other_deg0.753315885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78123.412337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.828151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3361569
X-RAY DIFFRACTIONr_chiral_restr0.0590.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021673
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 199 -
Rwork0.26 3845 -
all-4044 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58850.2375-0.00860.4495-0.36830.42550.0391-0.09930.01790.043-0.063-0.00730.02210.08130.02390.1695-0.02020.00930.1260.00930.008399.827-31.8331.525
20.76710.1133-0.01720.85180.15480.5169-0.0442-0.0157-0.04310.03930.03250.01920.079-0.09340.01170.1642-0.02440.01610.09500.0041102.084-35.660.784
32.70631.7488-0.60071.1562-0.52831.6866-0.0525-0.067-0.0341-0.018-0.0014-0.00910.0459-0.09910.05390.1396-0.03020.01530.12940.0390.035184.215-43.99427.664
40.58610.0003-0.03830.8783-0.080.41930.0252-0.04440.10370.04050.04880.2139-0.0296-0.0667-0.0740.1058-0.01990.03650.09930.02920.08682.412-20.79624.943
51.9832-0.73430.63421.2378-0.19861.39990.0590.0966-0.0894-0.0594-0.0233-0.10610.26570.1213-0.03570.16910.03960.02250.04770.00380.0537118.266-46.8999.837
60.40490.11350.08190.6499-0.05760.3108-0.0060.01040.0281-0.00240.0241-0.15130.02870.011-0.01810.12180.00450.02090.0681-0.01050.0562119.781-24.0925.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 80
2X-RAY DIFFRACTION2B1 - 80
3X-RAY DIFFRACTION3A127 - 167
4X-RAY DIFFRACTION4A81 - 126
5X-RAY DIFFRACTION4A168 - 462
6X-RAY DIFFRACTION5B127 - 167
7X-RAY DIFFRACTION6B81 - 126
8X-RAY DIFFRACTION6B168 - 462

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