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- PDB-2ypp: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 2ypp
Title3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with 3 tyrosine molecules
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
: / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_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_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)103,00919
Polymers101,4012
Non-polymers1,60817
Water2,774154
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)206,01838
Polymers202,8014
Non-polymers3,21734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area17420 Å2
ΔGint-334.5 kcal/mol
Surface area63530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.449, 203.449, 66.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2035-

HOH

21B-2029-

HOH

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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 / 3-DEOXY-D-ARAB INO- ...3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / 3-DEOXY-D-ARAB INO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE


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 , 6 types, 171 molecules

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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsL-TYROSINE (TYR): 3 TYROSINE LIGANDS ARE BOUND IN THE TWO MONOMERS OF THE ASYMMETRIC UNIT, 1 IN ...L-TYROSINE (TYR): 3 TYROSINE LIGANDS ARE BOUND IN THE TWO MONOMERS OF 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: 3.92 Å3/Da / Density % sol: 68.6 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 19, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953697 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.791
11-h,-k,l20.209
ReflectionResolution: 2.3→47.03 Å / Num. obs: 67961 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.13 / Rsym value: 0.126 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.237 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NV8

3nv8


Resolution: 2.3→44.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.144 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 11-12 AND CHAIN B RESIDUES 10-12 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.16375 3380 5 %RANDOM
Rwork0.13923 ---
obs0.14046 64572 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.829 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å20 Å20 Å2
2---4.42 Å20 Å2
3---8.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 93 154 7319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197361
X-RAY DIFFRACTIONr_bond_other_d0.0010.026998
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.96310021
X-RAY DIFFRACTIONr_angle_other_deg0.942316048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86823.429347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.267151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4691570
X-RAY DIFFRACTIONr_chiral_restr0.1190.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021689
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 218 -
Rwork0.184 4134 -
obs--85 %
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)
10.42920.2066-0.03570.1228-0.09630.3490.0632-0.1267-0.01220.0601-0.05070.0008-0.02030.032-0.01250.2003-0.01220.020.16640.00940.003599.229-31.282-1.662
20.65390.1555-0.14640.7034-0.13810.2367-0.0580.0411-0.0377-0.08790.05820.03410.0531-0.0425-0.00020.2161-0.04560.0140.1277-0.01020.0069101.741-35.786-32.46
32.11240.9115-0.77980.7655-0.67480.6333-0.0218-0.0073-0.06880.04310.0810.0255-0.0265-0.0792-0.05910.198-0.01460.01960.18810.05850.055383.982-43.831-5.633
40.45030.03860.05020.7173-0.21540.23650.0462-0.05030.03940.03870.04930.1929-0.0195-0.0307-0.09550.1664-0.00470.04160.14560.0340.071882.1-20.691-8.487
50.6669-0.55980.32852.3499-0.74970.99840.0328-0.0209-0.0051-0.0885-0.0576-0.2620.11830.08470.02490.18550.02530.03510.1250.02290.0813117.983-46.714-23.324
60.37940.1767-0.04130.6456-0.07230.1769-0.0344-0.0238-0.0286-0.030.0401-0.14410.01770.0074-0.00570.1762-0.00070.02420.125-0.01920.0392119.581-23.99-28.114
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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