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- PDB-5gmu: Crystal structure of chorismate mutase like domain of bifunctiona... -

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Basic information

Entry
Database: PDB / ID: 5gmu
TitleCrystal structure of chorismate mutase like domain of bifunctional DAHP synthase of Bacillus subtilis in complex with Chlorogenic acid
ComponentsProtein AroA(G)
KeywordsISOMERASE / Type II chorismate mutase / CML domain / Bifunctional DAHP synthase / Chlorogenic acid
Function / homology
Function and homology information


chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA ...Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7LH / Protein AroA(G)
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPratap, S. / Dev, A. / Sharma, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P.
CitationJournal: Sci Rep / Year: 2017
Title: Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site.
Authors: Pratap, S. / Dev, A. / Kumar, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P.
History
DepositionJul 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name
Revision 1.2Nov 8, 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: Protein AroA(G)
B: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6705
Polymers20,8622
Non-polymers8093
Water2,090116
1
A: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8833
Polymers10,4311
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area6930 Å2
MethodPISA
2
B: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7872
Polymers10,4311
Non-polymers3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.685, 47.049, 56.797
Angle α, β, γ (deg.)90.00, 107.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 4 - 87 / Label seq-ID: 4 - 87

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

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Components

#1: Protein Protein AroA(G)


Mass: 10430.755 Da / Num. of mol.: 2
Fragment: Chorismate Mutase type II like domain, UNP residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: aroA, BSU29750
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P39912, chorismate mutase
#2: Chemical ChemComp-7LH / (1R,3R,4S,5R)-3-[3-[3,4-bis(oxidanyl)phenyl]propanoyloxy]-1,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid


Mass: 356.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O9
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16372 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.58
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.76 / CC1/2: 0.926 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data processing
SCALAdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NVT

3nvt


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.897 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21523 875 5.3 %RANDOM
Rwork0.17514 ---
obs0.17728 15497 97.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 32.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-1.81 Å2
2--0.23 Å20 Å2
3---1.37 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 55 116 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191524
X-RAY DIFFRACTIONr_bond_other_d0.0020.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.7692.0092060
X-RAY DIFFRACTIONr_angle_other_deg0.94233351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9726.32287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.861510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
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_it2.1951.708710
X-RAY DIFFRACTIONr_mcbond_other2.1281.705709
X-RAY DIFFRACTIONr_mcangle_it3.0592.529892
X-RAY DIFFRACTIONr_mcangle_other3.0582.531893
X-RAY DIFFRACTIONr_scbond_it3.4232.216814
X-RAY DIFFRACTIONr_scbond_other3.3222.149756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0073.0721084
X-RAY DIFFRACTIONr_long_range_B_refined7.69523.2641828
X-RAY DIFFRACTIONr_long_range_B_other7.77422.0891726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5048 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 51 -
Rwork0.261 1031 -
obs--88.91 %
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)
11.9252-0.45770.1442.2274-0.14812.91530.02410.0610.05920.0233-0.0614-0.0305-0.04640.03750.03730.0405-0.02250.02420.0319-0.00750.01821.471-1.19513.882
21.49230.09990.38921.95441.45623.2236-0.0037-0.16930.0630.2307-0.0302-0.03270.1254-0.03140.03380.0820.00620.02810.04130.00610.02773.955-1.35621.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 88
2X-RAY DIFFRACTION2B2 - 88

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