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- PDB-2ypq: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with tryptop... -

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Basic information

Entry
Database: PDB / ID: 2ypq
Title3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with tryptophan and tyrosine bound
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
KeywordsTRANSFERASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / ALLOSTERY
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
: / PHOSPHATE ION / TRYPTOPHAN / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsBlackmore, N.J. / Reichau, S. / Jiao, W. / Hutton, R.D. / Baker, E.N. / Jameson, G.B. / Parker, E.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Three Sites and You are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis.
Authors: Blackmore, N.J. / Reichau, S. / Jiao, W. / Hutton, R.D. / Baker, E.N. / Jameson, G.B. / Parker, E.J.
History
DepositionOct 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,28419
Polymers101,4012
Non-polymers1,88317
Water1,45981
1
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
hetero molecules

A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,56838
Polymers202,8014
Non-polymers3,76634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area17410 Å2
ΔGint-236.4 kcal/mol
Surface area61220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.777, 202.777, 66.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 6 / Auth seq-ID: 20 - 462 / Label seq-ID: 20 - 462

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999981, 0.004529, 0.004095), (0.005621, 0.944789, 0.32763), (-0.002385, 0.327647, -0.944797)205.2106, 6.74024, -43.1598

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3- ...3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE


Mass: 50700.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 8 types, 98 molecules

#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsL-TRYPTOPHAN (TRP): 2 TRYPTOPHAN LIGANDS ARE PRESENT IN THE ASYMMETRIC UNIT IN EQUIVALENT SITES L- ...L-TRYPTOPHAN (TRP): 2 TRYPTOPHAN LIGANDS ARE PRESENT IN THE ASYMMETRIC UNIT IN EQUIVALENT SITES L-TYROSINE (TYR): 3 TYROSINE LIGANDS ARE PRESENT IN THE ASYMMETRIC UNIT, 1 IN SUBUNIT A AND 2 IN SUBUNIT B

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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: 3.91 Å3/Da / Density % sol: 68.52 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 15% V/V GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542
DetectorType: RAXIS / Detector: IMAGE PLATE
RadiationMonochromator: AXCO PX70 FOCUSSING AND MONOCHROMATING CAPILLARY OPTICS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.8→39.72 Å / Num. obs: 39770 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4.06 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
d*TREKdata reduction
CrystalClear1.3.6data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NV8

3nv8


Resolution: 2.76→175.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.281 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24888 1925 4.8 %RANDOM
Rwork0.1773 ---
obs0.18081 37979 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.76→175.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7029 0 117 81 7227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197281
X-RAY DIFFRACTIONr_bond_other_d0.0010.024874
X-RAY DIFFRACTIONr_angle_refined_deg3.3481.9629903
X-RAY DIFFRACTIONr_angle_other_deg1.494311830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6755913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61423.284335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.967151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3611568
X-RAY DIFFRACTIONr_chiral_restr0.1710.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0218173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021472
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 5697 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.565
2Bloose positional0.565
1Aloose thermal6.6310
2Bloose thermal6.6310
LS refinement shellResolution: 2.76→2.831 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 127 -
Rwork0.182 2242 -
obs--79.93 %

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