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- PDB-6bmc: The structure of a dimeric type II DAH7PS associated with pyocyan... -

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Basic information

Entry
Database: PDB / ID: 6bmc
TitleThe structure of a dimeric type II DAH7PS associated with pyocyanin biosynthesis in Pseudomonas aeruginosa
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAH7PS / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway / pyocyanin biosynthesis
Function / homologyDAHP synthetase, class II / Class-II DAHP synthetase family / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aromatic amino acid family biosynthetic process / Aldolase-type TIM barrel / : / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSterritt, O.W. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biosci. Rep. / Year: 2018
Title: Structural and functional characterisation of the entry point to pyocyanin biosynthesis inPseudomonas aeruginosadefines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass.
Authors: Sterritt, O.W. / Lang, E.J.M. / Kessans, S.A. / Ryan, T.M. / Demeler, B. / Jameson, G.B. / Parker, E.J.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Oct 4, 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 / 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

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2697
Polymers88,7792
Non-polymers4895
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Dimer-tetramer equilibrium
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-53 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.757, 169.722, 170.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phospho-2-dehydro-3-deoxyheptonate aldolase / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase


Mass: 44389.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: phzC, aroH_3, AOY09_05716, CAZ10_37830, PAERUG_E15_London_28_01_14_08300
Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: G3XCJ9, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1-0.4 M NaF, 1 mM CoCl2, 1 mM PE, 16-22 % PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95363 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95363 Å / Relative weight: 1
ReflectionResolution: 2.7→85.27 Å / Num. obs: 21959 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 73.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.064 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 10 % / Rmerge(I) obs: 2.619 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2879 / CC1/2: 0.461 / Rpim(I) all: 1.28 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
autoXDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UXM

5uxm


Resolution: 2.7→85.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28978 1086 5 %RANDOM
Rwork0.24756 ---
obs0.24961 20845 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.938 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2---0.85 Å20 Å2
3----2.66 Å2
Refinement stepCycle: 1 / Resolution: 2.7→85.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5667 0 23 13 5703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195793
X-RAY DIFFRACTIONr_bond_other_d00.025534
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.9687888
X-RAY DIFFRACTIONr_angle_other_deg3.621312611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60322.083240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07515894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4461568
X-RAY DIFFRACTIONr_chiral_restr0.0540.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216638
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021306
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_it2.5899.0123034
X-RAY DIFFRACTIONr_mcbond_other2.5899.0123033
X-RAY DIFFRACTIONr_mcangle_it4.43513.5083782
X-RAY DIFFRACTIONr_mcangle_other4.43413.5083783
X-RAY DIFFRACTIONr_scbond_it2.7199.1592759
X-RAY DIFFRACTIONr_scbond_other2.7089.1592758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.53513.6474106
X-RAY DIFFRACTIONr_long_range_B_refined7.15471.3086608
X-RAY DIFFRACTIONr_long_range_B_other7.15571.3136609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 88 -
Rwork0.455 1497 -
obs--100 %

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