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- PDB-3nv8: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 3nv8
TitleThe structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free)
ComponentsProbable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
KeywordsTRANSFERASE / DAH7P synthase / Shikimate pathway / Aromatic amino-acid biosynthesis / Evolutionary relationships / Augmented TIM-barrel structure / TIM barrel / Aldolase / Cytosol
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
: / PHOSPHOENOLPYRUVATE / PHOSPHATE ION / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsParker, E.J. / Jameson, G.B. / Jiao, W. / Hutton, R.H. / Webby, C.J. / Baker, E.N. / Baker, H.M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis
Authors: Webby, C.J. / Jiao, W. / Hutton, R.D. / Blackmore, N.J. / Baker, H.M. / Baker, E.N. / Jameson, G.B. / Parker, E.J.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes
Authors: Webby, C.J. / Baker, H.M. / Lott, J.S. / Baker, E.N. / Parker, E.J.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Nov 1, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,90616
Polymers101,6572
Non-polymers1,24914
Water5,044280
1
A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules

A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,81232
Polymers203,3144
Non-polymers2,49828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area11440 Å2
ΔGint-92 kcal/mol
Surface area66070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.538, 203.538, 66.422
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
11B-591-

HOH

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: 22 - 464

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG / DAHP synthetase / phenylalanine-repressible


Mass: 50828.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: RV2178C / Plasmid: PPROEXHTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 7 types, 294 molecules

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


Mass: 96.063 Da / Num. of mol.: 3 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.91 Å3/Da / Density % sol: 68.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 11, 2009 / Details: AXCO PX70
RadiationMonochromator: AXCO PX70 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→39.4 Å / Num. all: 73037 / Num. obs: 73037 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.11 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7137 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGF (stripped of ligands and waters)

3kgf


Resolution: 2.25→39.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.262 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3648 5 %RANDOM
Rwork0.17997 ---
obs0.18137 69535 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7098 0 69 280 7447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217398
X-RAY DIFFRACTIONr_bond_other_d00.024976
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.96510077
X-RAY DIFFRACTIONr_angle_other_deg1.148312082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3355942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06423.275342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.497151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581573
X-RAY DIFFRACTIONr_chiral_restr0.1260.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
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_it1.1811.54676
X-RAY DIFFRACTIONr_mcbond_other0.321.51876
X-RAY DIFFRACTIONr_mcangle_it1.96327528
X-RAY DIFFRACTIONr_scbond_it2.99132722
X-RAY DIFFRACTIONr_scangle_it4.2674.52549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5608 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.45
loose thermal1.9710
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 247 -
Rwork0.185 5011 -
obs--95.24 %
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)
11.0421-0.1165-0.04241.57360.08151.07140.0077-0.056-0.09310.0121-0.0107-0.11890.1060.1630.0030.02580.0030.00310.0380.00370.020399.6072-31.8502-1.7785
21.0030.0270.18631.84720.19411.3068-0.0486-0.0795-0.0887-0.02770.04310.24140.1322-0.23150.00540.0192-0.02220.00050.04650.01350.04101.5847-36.2281-31.9407
35.33273.5419-0.54943.6456-0.6730.17830.0378-0.2426-0.10230.061-0.01190.16140.0285-0.0662-0.02580.0648-0.04260.00750.09290.00990.054784.067-43.8306-5.7087
40.8907-0.5241-0.13691.1787-0.26421.0973-0.01440.05910.0439-0.03710.03670.1832-0.0214-0.1678-0.02240.041-0.01760.01480.0374-0.00430.080981.9913-20.798-8.6902
52.9665-1.26340.07252.4669-0.70630.4526-0.00020.1271-0.14190.006-0.0554-0.25170.07360.11340.05560.06110.0311-0.01810.0631-0.0320.0695117.9795-46.7233-23.7033
60.83050.5643-0.39841.36260.24081.1196-0.0002-0.12710.00230.08030.0129-0.21040.03890.1538-0.01270.02020.0087-0.00920.032-0.01510.0663119.7828-23.9387-28.1261
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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