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- PDB-5hud: Non-covalent complex of and DAHP synthase and chorismate mutase f... -

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Basic information

Entry
Database: PDB / ID: 5hud
TitleNon-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog
Components
  • 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
  • Chorismate mutase
KeywordsTRANSFERASE/ISOMERASE / chorismate mutase / DAHP synthase / shikimate pathway / complex / Transferase-Isomerase complex
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding
Similarity search - Function
Chorismate mutase, high GC Gram-positive bacteria/archaeal / DAHP synthetase, class II / Class-II DAHP synthetase family / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type ...Chorismate mutase, high GC Gram-positive bacteria/archaeal / DAHP synthetase, class II / Class-II DAHP synthetase family / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / TRYPTOPHAN / Chem-TSA / Phospho-2-dehydro-3-deoxyheptonate aldolase / Chorismate mutase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBurschowsky, D. / Heim, J.B. / Thorbjoernsrud, H.V. / Krengel, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
The Research Council of Norway214037 Norway
CitationJournal: Biochemistry / Year: 2018
Title: Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp.
Authors: Burschowsky, D. / Thorbjornsrud, H.V. / Heim, J.B. / Fahrig-Kamarauskaite, J.R. / Wurth-Roderer, K. / Kast, P. / Krengel, U.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
B: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
C: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
D: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
E: Chorismate mutase
F: Chorismate mutase
G: Chorismate mutase
H: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,233127
Polymers248,8648
Non-polymers13,369119
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50130 Å2
ΔGint-102 kcal/mol
Surface area79870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.622, 110.481, 134.652
Angle α, β, γ (deg.)90.00, 101.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase


Mass: 52150.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl2178 / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: Q8NNL5
#2: Protein
Chorismate mutase


Mass: 10065.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl0853 / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: Q8NS29, chorismate mutase

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Non-polymers , 9 types, 898 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#9: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical
ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12O6
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro- ...Details: 100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.1→131.99 Å / Num. obs: 190339 / % possible obs: 96.7 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 4.79
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.24 % / Rmerge(I) obs: 1.763 / Mean I/σ(I) obs: 0.44 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHASERphasing
Aimlessdata scaling
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1A

2w1a


Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.867 / SU B: 10.127 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 8846 4.9 %RANDOM
Rwork0.24952 ---
obs0.25191 170847 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.09 Å2
2---1.03 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16558 0 871 779 18208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917692
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217019
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.99123699
X-RAY DIFFRACTIONr_angle_other_deg0.986339134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09152138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92423.689835
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.337152915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.18715169
X-RAY DIFFRACTIONr_chiral_restr0.0790.22605
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119615
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023920
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_it1.9263.2118570
X-RAY DIFFRACTIONr_mcbond_other1.9263.218569
X-RAY DIFFRACTIONr_mcangle_it3.1544.80210699
X-RAY DIFFRACTIONr_mcangle_other3.1544.80210700
X-RAY DIFFRACTIONr_scbond_it2.1653.6029122
X-RAY DIFFRACTIONr_scbond_other2.1653.6029122
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5525.24713000
X-RAY DIFFRACTIONr_long_range_B_refined5.825.46819759
X-RAY DIFFRACTIONr_long_range_B_other5.825.4719760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 588 -
Rwork0.401 11500 -
obs--89.53 %

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