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- PDB-5e5g: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-trypt... -

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Basic information

Entry
Database: PDB / ID: 5e5g
Title3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the tryptophan and phenylalanine binding sites
Components3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
KeywordsTRANSFERASE / allosteric regulation / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway
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-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: 1.95 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 8, 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
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)103,06413
Polymers101,6572
Non-polymers1,40711
Water11,674648
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)206,12826
Polymers203,3144
Non-polymers2,81422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area14050 Å2
ΔGint-264 kcal/mol
Surface area63000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.002, 205.002, 66.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#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
#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-DTR / D-TRYPTOPHAN


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


Mass: 18.015 Da / Num. of mol.: 648 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 293 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 10 MM D-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: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→47.25 Å / Num. obs: 116470 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.047 / Net I/σ(I): 14.1 / Num. measured all: 1300419
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
1.95-1.988.51.4891.54820456940.5180.53399.7
10.68-47.259.80.02853.3754776810.00998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3nv8


Resolution: 1.95→47.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.1645 / FOM work R set: 0.9079 / SU B: 3.219 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0247 / SU Rfree: 0.0224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 5798 5 %RANDOM
Rwork0.1677 ---
obs0.1685 110646 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.6 Å2 / Biso mean: 31.686 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0 Å2
2---0.82 Å2-0 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 1.95→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 82 648 7691
Biso mean--35.94 38.49 -
Num. residues----915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0197264
X-RAY DIFFRACTIONr_bond_other_d0.0010.026871
X-RAY DIFFRACTIONr_angle_refined_deg0.7151.979899
X-RAY DIFFRACTIONr_angle_other_deg0.571315728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4465922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62923.354328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.681151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651567
X-RAY DIFFRACTIONr_chiral_restr0.0360.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0218344
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021671
X-RAY DIFFRACTIONr_mcbond_it1.6961.8713691
X-RAY DIFFRACTIONr_mcbond_other1.6941.873690
X-RAY DIFFRACTIONr_mcangle_it2.8112.7844609
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 421 -
Rwork0.276 8129 -
all-8550 -
obs--99.65 %
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)
10.62180.3530.04180.2113-0.00670.51430.0768-0.1527-0.00980.0574-0.06150.00260.00890.055-0.01540.2006-0.01280.01630.14190.02110.006799.275-31.56-1.639
20.66480.0174-0.11630.4174-0.17330.6117-0.00260.0371-0.0589-0.02960.01520.00280.0793-0.0746-0.01270.1749-0.00970.00780.069-0.00590.0073102.879-35.746-32.686
32.45322.0982-1.41211.8586-1.280.8951-0.09260.0602-0.0693-0.02520.1113-0.0104-0.0021-0.1029-0.01880.1916-0.03340.00760.13380.05220.053984.528-44.334-5.835
40.7375-0.00890.07960.8957-0.19340.48010.0341-0.09550.08450.05430.03380.21-0.0441-0.0767-0.06780.1421-0.01590.03490.10450.01470.066682.668-21.149-8.504
50.535-1.0230.39392.0555-0.5121.42120.02090.02840.09090.0419-0.0544-0.23610.10360.08960.03350.18480.0155-0.01210.07570.02120.1172118.769-47.041-23.684
60.50860.10260.02360.75620.02910.38130.006-0.01080.0213-0.030.0109-0.18190.01990.0316-0.01690.13950.00570.02050.0567-0.01120.0505120.144-24.32-28.28
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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