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- PDB-5e40: 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 5.0E+40
Title3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site
Components3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
KeywordsTRANSFERASE / amino acid / allosteric regulation / shikimate pathway / 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase
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-TYROSINE / : / 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 / molecular replacement / Resolution: 2.05 Å
AuthorsReichau, S. / Jiao, W. / Parker, E.J.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
New Zealand Marsden GrantUOC1105 New Zealand
Maurice Wilkins Center 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 5, 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_struct_oper_list / struct_conn
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_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)102,70112
Polymers101,6572
Non-polymers1,04510
Water9,674537
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)205,40324
Polymers203,3144
Non-polymers2,08920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area15160 Å2
ΔGint-277 kcal/mol
Surface area64070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.451, 205.451, 66.803
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-633-

HOH

21B-618-

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 , 5 types, 547 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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-DTY / D-TYROSINE


Type: D-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and ...Details: 0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and 24 hours before crystal freezing, respectively

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 4, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→19.85 Å / Num. obs: 101083 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.056 / Net I/σ(I): 11.8 / Num. measured all: 762663
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.097.51.0262.13777550070.6080.398100
11.23-19.856.90.02838.936935370.9990.01181.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NV8

3nv8


Resolution: 2.05→19.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1726 / FOM work R set: 0.8952 / SU B: 2.831 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5046 5 %RANDOM
Rwork0.1941 ---
obs0.1948 96017 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.95 Å2 / Biso mean: 27.469 Å2 / Biso min: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refinement stepCycle: final / Resolution: 2.05→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 54 537 7636
Biso mean--39.82 38.87 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197324
X-RAY DIFFRACTIONr_bond_other_d0.0050.026953
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9649981
X-RAY DIFFRACTIONr_angle_other_deg0.806315939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37323.411343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.761151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241570
X-RAY DIFFRACTIONr_chiral_restr0.0610.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218427
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021687
X-RAY DIFFRACTIONr_mcbond_it1.2792.6693702
X-RAY DIFFRACTIONr_mcbond_other1.2792.6693701
X-RAY DIFFRACTIONr_mcangle_it2.3393.9944627
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 404 -
Rwork0.248 7036 -
all-7440 -
obs--99.97 %

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