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- PDB-9bt7: Crystal structure of Chorismate Mutase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 9bt7
TitleCrystal structure of Chorismate Mutase from Mycobacterium tuberculosis in complex with the cyclic peptide inhibitor D1.3
Components
  • Cyclic peptide inhibitor D1.3
  • Secreted chorismate mutase
KeywordsISOMERASE / Chorismate Mutase / Mycobacterium tuberculosis / cyclic peptide inhibitor
Function / homology
Function and homology information


salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / extracellular region
Similarity search - Function
Chorismate mutase, periplasmic / : / 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
Similarity search - Domain/homology
Secreted chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, L. / Lovell, S. / Battaile, K.P. / Inglese, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD030394 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)1ZIATR000053 United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Active- and Allosteric-Site Cyclic Peptide Inhibitors of Secreted M. tuberculosis Chorismate Mutase.
Authors: van Neer, R.H.P. / Dranchak, P.K. / Aitha, M. / Liu, L. / Carlson, E.K. / Jacobsen, I.E. / Battaile, K. / Fang, Y. / Tao, D. / Rai, G. / Padia, J. / Lovell, S. / Suga, H. / Inglese, J.
History
DepositionMay 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted chorismate mutase
B: Secreted chorismate mutase
C: Cyclic peptide inhibitor D1.3
D: Cyclic peptide inhibitor D1.3


Theoretical massNumber of molelcules
Total (without water)49,7194
Polymers49,7194
Non-polymers00
Water4,720262
1
A: Secreted chorismate mutase
D: Cyclic peptide inhibitor D1.3


Theoretical massNumber of molelcules
Total (without water)24,8592
Polymers24,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-5 kcal/mol
Surface area9310 Å2
MethodPISA
2
B: Secreted chorismate mutase
C: Cyclic peptide inhibitor D1.3


Theoretical massNumber of molelcules
Total (without water)24,8592
Polymers24,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.186, 71.102, 71.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Secreted chorismate mutase / CM / *MtCM


Mass: 22973.375 Da / Num. of mol.: 2 / Fragment: D34-A199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1885c / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIB9, chorismate mutase
#2: Protein/peptide Cyclic peptide inhibitor D1.3


Mass: 1886.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ H7: (25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2M Ammonium Sulfate), chorismate mutase at 10 mg/mL. plate 12878, well H7 drop 2. Puck: PSL-0513, Cryo: 80% crystallant and 20% PEG 200 .

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→71.6 Å / Num. obs: 33927 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.069 / Rrim(I) all: 0.216 / Χ2: 1 / Net I/σ(I): 8.5 / Num. measured all: 315844
Reflection shellResolution: 1.8→1.85 Å / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 1.625 / Num. measured all: 22687 / Num. unique obs: 2458 / CC1/2: 0.636 / Rpim(I) all: 0.557 / Rrim(I) all: 1.72 / Χ2: 1.01 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.95 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1785 5.27 %
Rwork0.1756 --
obs0.1773 33845 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 262 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062928
X-RAY DIFFRACTIONf_angle_d0.7863992
X-RAY DIFFRACTIONf_dihedral_angle_d13.8071105
X-RAY DIFFRACTIONf_chiral_restr0.047429
X-RAY DIFFRACTIONf_plane_restr0.01534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.34561840.28522367X-RAY DIFFRACTION100
1.85-1.90.29641320.23352430X-RAY DIFFRACTION100
1.9-1.960.23061260.20722446X-RAY DIFFRACTION100
1.96-2.030.23641340.19082430X-RAY DIFFRACTION100
2.03-2.120.2175930.18162484X-RAY DIFFRACTION100
2.12-2.210.24551040.17772476X-RAY DIFFRACTION100
2.21-2.330.20431670.16222412X-RAY DIFFRACTION100
2.33-2.480.19591680.16622421X-RAY DIFFRACTION100
2.48-2.670.23341190.16862493X-RAY DIFFRACTION100
2.67-2.930.21341240.1762480X-RAY DIFFRACTION100
2.93-3.360.20951250.17662508X-RAY DIFFRACTION100
3.36-4.230.17361510.15372505X-RAY DIFFRACTION100
4.23-49.950.17611580.16792608X-RAY DIFFRACTION99
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)
11.4715-1.3158-0.11272.0122-0.09950.5250.02180.0920.1076-0.0825-0.0582-0.2378-0.04260.06940.02110.1255-0.0256-0.01040.145-0.020.154721.89328.40787.5613
20.8409-0.27450.54155.917-1.71121.3888-0.08850.01430.04960.38110.0965-0.4345-0.19560.1166-0.04550.2112-0.0085-0.02620.2325-0.03010.173520.1139.245421.5181
30.0231-0.13570.09661.88870.02370.5941-0.00530.00490.0184-0.07130.0107-0.1013-0.0430.0399-0.02070.1248-0.0132-0.00350.1673-0.00440.139221.012522.888910.6008
42.4736-0.79720.52141.5945-0.09241.25580.0347-0.00160.04070.1053-0.0340.0161-0.15620.0538-0.00090.1598-0.00420.00470.133-0.00850.154218.736141.4239.8015
54.5636-3.5816-3.54253.08942.54582.94180.29080.4195-0.0743-0.4226-0.3180.3209-0.4266-0.36360.04290.17060.0085-0.03390.23160.00590.18126.649836.5279-1.1182
61.38640.17110.29172.20570.05121.52090.10170.0362-0.02670.075-0.11660.07690.0288-0.25690.02760.1569-0.0087-0.00560.16140.00720.111810.872830.01895.3938
70.5836-0.4625-0.03682.66771.43981.5242-0.0298-0.0153-0.08430.0241-0.06060.3170.0296-0.01730.05410.1519-0.00540.00310.15530.02280.166513.37411.826415.6783
81.13141.080.57015.97680.6471.23810.1502-0.0916-0.19110.4521-0.22560.09210.2025-0.03020.08870.1477-0.004-0.00650.19090.01010.172226.591-8.509320.4542
90.3999-0.71820.2531.7937-0.12650.3548-0.0388-0.0446-0.09390.06350.06080.17140.018-0.0472-0.01570.1293-0.01410.00710.1634-0.0010.171116.26956.199914.7263
101.9325-1.2209-0.82812.63920.64042.96940.0242-0.0484-0.02830.19680.02990.10070.2488-0.0092-0.09780.1488-0.0056-0.00820.14090.01180.16117.119-11.898714.9669
113.3334-2.357-1.40282.81961.25911.99710.04360.6174-0.1883-0.1374-0.27670.25610.1177-0.32290.15260.206-0.0113-0.04640.1921-0.03050.150612.6213-9.4285-1.7875
121.8513-0.75260.36682.2212-0.2751.28170.0830.22720.0072-0.1487-0.1749-0.0285-0.08410.06230.10030.1706-0.0156-0.02190.1617-0.00330.15416.3774-2.11684.0393
131.0002-0.84340.44641.524-0.32941.5280.0151-0.04970.07970.0533-0.0172-0.2484-0.13060.1314-0.03610.1595-0.0084-0.01690.1811-0.0060.209632.82173.451215.6423
140.9163-0.47560.03852.71821.60781.8605-0.0727-0.2565-0.02970.70940.13390.0828-0.0424-0.0053-0.06970.29610.03890.01810.2206-0.0030.150813.912126.490725.6748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 196 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 69 )
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 90 )
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 130 )
10X-RAY DIFFRACTION10chain 'B' and (resid 131 through 157 )
11X-RAY DIFFRACTION11chain 'B' and (resid 158 through 174 )
12X-RAY DIFFRACTION12chain 'B' and (resid 175 through 196 )
13X-RAY DIFFRACTION13chain 'C'
14X-RAY DIFFRACTION14chain 'D'

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