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- PDB-6oyh: Crystal structure of MraY bound to carbacaprazamycin -

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Basic information

Entry
Database: PDB / ID: 6oyh
TitleCrystal structure of MraY bound to carbacaprazamycin
Components
  • MraYAA nanobody
  • Phospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsMEMBRANE PROTEIN/TRANSFERASE / peptidoglycan biosynthesis / antibiotic target / integral membrane enzyme / translocase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / metal ion binding ...phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Chem-NK4 / Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesLama glama (llama)
Aquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMashalidis, E.H. / Lee, S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2019
Title: Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Authors: Mashalidis, E.H. / Kaeser, B. / Terasawa, Y. / Katsuyama, A. / Kwon, D.Y. / Lee, K. / Hong, J. / Ichikawa, S. / Lee, S.Y.
History
DepositionMay 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: MraYAA nanobody
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
G: MraYAA nanobody
C: Phospho-N-acetylmuramoyl-pentapeptide-transferase
F: MraYAA nanobody
B: Phospho-N-acetylmuramoyl-pentapeptide-transferase
H: MraYAA nanobody
D: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,24112
Polymers224,0498
Non-polymers3,1924
Water28816
1
E: MraYAA nanobody
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8103
Polymers56,0122
Non-polymers7981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: MraYAA nanobody
C: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8103
Polymers56,0122
Non-polymers7981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: MraYAA nanobody
B: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8103
Polymers56,0122
Non-polymers7981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: MraYAA nanobody
D: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8103
Polymers56,0122
Non-polymers7981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.888, 129.578, 129.428
Angle α, β, γ (deg.)90.00, 109.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
MraYAA nanobody


Mass: 15057.651 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein
Phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-MurNAc-pentapeptide phosphotransferase


Mass: 40954.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: mraY, aq_053 / Production host: Escherichia coli (E. coli)
References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase
#3: Chemical
ChemComp-NK4 / (5S)-5'-O-(5-amino-5-deoxy-beta-D-ribofuranosyl)-5'-C-[(2S,5S,6S)-5-carboxy-6-heptadecyl-1,4-dimethyl-3-oxo-1,4-diazepan-2-yl]uridine


Mass: 797.976 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H67N5O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 22% polyethylene glycol 4000, 0.2 M potassium thiocyanate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→43.941 Å / Num. obs: 61002 / % possible obs: 98.7 % / Redundancy: 4.3 % / CC1/2: 0.892 / Rpim(I) all: 0.07917 / Net I/σ(I): 12.86
Reflection shellResolution: 2.95→3.055 Å / Num. unique obs: 5579 / CC1/2: 0.444 / Rpim(I) all: 0.636

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKR

5ckr


Resolution: 2.95→43.941 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 2627 4.32 %
Rwork0.2485 --
obs0.2494 60825 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→43.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13611 0 224 16 13851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514166
X-RAY DIFFRACTIONf_angle_d0.78919351
X-RAY DIFFRACTIONf_dihedral_angle_d13.1044664
X-RAY DIFFRACTIONf_chiral_restr0.0452360
X-RAY DIFFRACTIONf_plane_restr0.0052339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.00360.37431190.3692716X-RAY DIFFRACTION88
3.0036-3.06140.33271380.34272913X-RAY DIFFRACTION95
3.0614-3.12390.34691260.33163016X-RAY DIFFRACTION98
3.1239-3.19180.3581420.31243087X-RAY DIFFRACTION100
3.1918-3.2660.27881390.29193094X-RAY DIFFRACTION100
3.266-3.34760.32681360.28393079X-RAY DIFFRACTION100
3.3476-3.43810.30761460.27843082X-RAY DIFFRACTION100
3.4381-3.53920.27671330.27173081X-RAY DIFFRACTION100
3.5392-3.65340.26391350.26673100X-RAY DIFFRACTION100
3.6534-3.78390.30541460.26923113X-RAY DIFFRACTION99
3.7839-3.93530.28891310.25213077X-RAY DIFFRACTION99
3.9353-4.11430.25841490.22443066X-RAY DIFFRACTION100
4.1143-4.33110.21981370.20953119X-RAY DIFFRACTION100
4.3311-4.60210.22531370.19993090X-RAY DIFFRACTION100
4.6021-4.9570.23491470.19293105X-RAY DIFFRACTION100
4.957-5.45510.25861380.22333099X-RAY DIFFRACTION100
5.4551-6.24250.29441430.25773113X-RAY DIFFRACTION100
6.2425-7.85760.25351400.24333131X-RAY DIFFRACTION100
7.8576-43.94570.24611450.25313117X-RAY DIFFRACTION98
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)
12.9549-0.9708-1.03484.11652.32893.74040.10750.1945-0.1259-0.3813-0.18960.1642-0.2415-0.18280.04940.47690.0238-0.03530.33-0.01530.3778291.60026.6763231.7523
22.07670.31210.51522.36781.46862.50340.00510.209-0.0462-0.30980.6975-0.7439-0.04691.204-0.66670.6459-0.04380.15340.9128-0.33130.7277322.150113.0705240.4197
32.88380.7526-0.57832.44820.04160.5631-0.04270.65640.1959-0.54570.1697-0.0338-0.2255-0.1214-0.0920.7848-0.1091-0.01330.63160.11160.4122271.64175.7272289.9891
41.8707-0.12720.41882.1596-0.15092.10120.01790.06680.1119-0.4516-0.3074-0.6853-0.37040.66330.26070.6402-0.11380.09180.71960.22060.6764301.81794.103301.5852
54.6086-1.4782-2.34081.84162.56516.09760.03550.0525-0.1025-0.1036-0.1765-0.0399-0.2898-0.28880.16870.51460.0505-0.03780.3579-0.06440.6166271.472832.2952258.8495
65.1363-0.577-1.64725.58414.03585.2813-0.1336-0.01810.22920.06340.4956-0.35960.02960.5429-0.36050.4203-0.0098-0.04550.549-0.01730.418313.192136.2853274.5275
76.02922.5433-3.3733.7745-2.37826.1684-0.00690.40250.3349-0.39880.2739-0.0009-0.1903-0.2506-0.20210.40940.0296-0.00030.41630.0410.3612251.2863-13.3531321.5554
86.13611.0835-2.65593.0756-0.70694.20420.2209-0.26810.18530.0478-0.5697-0.3271-0.15360.62870.22060.5296-0.0763-0.09490.67530.27720.7254292.9911-20.3275335.5103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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