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- PDB-6pbj: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 6pbj
TitleThe structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro mutation
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAH7PS / Allostery / shipmate pathway / TIM barrel
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
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phospho-2-dehydro-3-deoxyheptonate aldolase / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiao, W. / Fan, Y. / Blackmore, N.J. / Parker, E.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis .
Authors: Jiao, W. / Fan, Y. / Blackmore, N.J. / Parker, E.J.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44523
Polymers101,7372
Non-polymers1,70821
Water9,530529
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)206,88946
Polymers203,4744
Non-polymers3,41542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)204.251, 204.251, 66.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

21B-611-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: -1 - 462 / Label seq-ID: 1 - 464

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.46802, 0.841486, 0.269924), (0.842294, -0.517183, 0.151862), (0.26739, 0.15628, -0.950831)-97.537643, 177.271194, -21.693951

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 50868.457 Da / Num. of mol.: 2 / Mutation: G190P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aroG_1, ERS027644_03091, ERS031537_02142, ERS124361_01166
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T9FW33, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 7 types, 550 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM BTP, 150 mM NaCl, 0.5 mM TCEP, 0.2 mM PEP, 0.1 mM MnCl2, 2M Li2SO4, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11h,-h-k,-l10.611
11h+k,-k,-l20.389
ReflectionResolution: 1.9→51.06 Å / Num. obs: 124730 / % possible obs: 99.9 % / Redundancy: 14.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.035 / Rrim(I) all: 0.136 / Net I/σ(I): 16.9 / Num. measured all: 1783055 / Scaling rejects: 491
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.937.41.3334517160990.3450.4881.4291.699.5
10.41-51.0618.90.039155078210.9990.0090.04155.897.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.2.17data scaling
PDB_EXTRACT3.24data extraction
MOSFLM7.1.0data reduction
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NV8

3nv8


Resolution: 1.9→36.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.229 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 6226 5 %RANDOM
Rwork0.1577 ---
obs0.1588 118485 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.26 Å2 / Biso mean: 20.536 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2--2.05 Å20 Å2
3----4.11 Å2
Refinement stepCycle: final / Resolution: 1.9→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 89 529 7097
Biso mean--31.71 28.23 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136810
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176316
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.649288
X-RAY DIFFRACTIONr_angle_other_deg1.3581.56914568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63121.222352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.063151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0711558
X-RAY DIFFRACTIONr_chiral_restr0.0840.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027733
X-RAY DIFFRACTIONr_gen_planes_other00.021397
Refine LS restraints NCS

Ens-ID: 1 / Number: 12838 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.506 440 -
Rwork0.461 8668 -
all-9108 -
obs--99.25 %

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