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- PDB-5e7z: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 5e7z
Title3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D/L-tryptophan and D-phenylalanine
Components3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
KeywordsTRANSFERASE / shikimate pathway / allosteric regulation
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 / D-TRYPTOPHAN / : / TRYPTOPHAN / 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: 2.4 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 13, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)103,39015
Polymers101,6572
Non-polymers1,73313
Water2,360131
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)206,78130
Polymers203,3144
Non-polymers3,46726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area15220 Å2
ΔGint-242 kcal/mol
Surface area63490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.357, 206.357, 66.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 , 7 types, 144 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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-DTR / D-TRYPTOPHAN


Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#6: Chemical ChemComp-DPN / D-PHENYLALANINE


Type: D-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLIZATION CONDITIONS: 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 0.25 MILLIM D- ...Details: CRYSTALLIZATION CONDITIONS: 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 0.25 MILLIM D-PHENYLALANINE AND 2.5 MILLIM TRYPTOPHAN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.69
11-h,-k,l20.31
ReflectionResolution: 2.33→47.55 Å / Num. obs: 71044 / % possible obs: 100 % / Redundancy: 12.3 % / Net I/σ(I): 4.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3nv8


Resolution: 2.4→47.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.175 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.161 3128 4.9 %RANDOM
Rwork0.137 ---
obs0.138 60738 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 112 131 7273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197297
X-RAY DIFFRACTIONr_bond_other_d0.0060.026937
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9679932
X-RAY DIFFRACTIONr_angle_other_deg1.21315880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90923.412337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.159151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.091568
X-RAY DIFFRACTIONr_chiral_restr0.1080.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218350
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 225 -
Rwork0.185 4432 -
obs--99.76 %
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)
10.0720.0672-0.05140.4784-0.08090.04150.0089-0.0170.0035-0.082-0.00860.01810.00690.0005-0.00030.0495-0.03250.00080.0584-0.01960.0106-78.027370.9088-31.7047
20.32730.04760.05190.44420.11640.3434-0.0021-0.0149-0.0178-0.00450.00120.01180.0705-0.00270.00090.0349-0.03290.00190.0605-0.00150.0028-82.958871.3427-0.6997
30.07290.26960.07543.12491.02270.33890.02750.0323-0.03050.0366-0.03550.00250.0126-0.02530.00810.0661-0.0185-0.02830.0479-0.01330.0293-81.266151.4291-27.6277
40.28030.11240.07890.29060.07310.09770.01320.0208-0.0676-0.0320.0187-0.07180.0160.0079-0.03190.0352-0.02980.01410.0395-0.02560.0406-60.066561.6513-24.6653
52.2207-0.47040.17310.1168-0.14950.98420.03240.0350.1374-0.01290.0272-0.0214-0.0156-0.1497-0.05960.0203-0.0271-0.00260.07650.00490.08-100.660179.6302-9.6718
60.25610.076-0.03070.2121-0.03910.05080.0075-0.00870.0771-0.00330.00140.04890.0158-0.0182-0.00890.0174-0.02870.010.0528-0.01090.045-81.46492.2661-5.1707
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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