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- PDB-5jnq: MraY tunicamycin complex -

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Basic information

Entry
Database: PDB / ID: 5jnq
TitleMraY tunicamycin complex
ComponentsPhospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsTransferase/Antibiotic / Membrane protein / antibiotic / PNPT / Transferase-Antibiotic complex
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / cell cycle / cell division / 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
PALMITIC ACID / Tunicamycin / Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesClostridium bolteae 90A9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJohansson, P.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: MraY-antibiotic complex reveals details of tunicamycin mode of action.
Authors: Hakulinen, J.K. / Hering, J. / Branden, G. / Chen, H. / Snijder, A. / Ek, M. / Johansson, P.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5695
Polymers40,9471
Non-polymers1,6224
Water543
1
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules

A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,13810
Polymers81,8942
Non-polymers3,2448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_589x,-y+3,-z+41
Unit cell
Length a, b, c (Å)92.640, 105.540, 134.960
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-N-acetylmuramoyl-pentapeptide-transferase / / UDP-MurNAc-pentapeptide phosphotransferase


Mass: 40947.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium bolteae 90A9 (bacteria) / Gene: mraY, HMPREF1085_00623 / Production host: Escherichia coli (E. coli)
References: UniProt: R0BTE9, phospho-N-acetylmuramoyl-pentapeptide-transferase
#2: Chemical ChemComp-TUM / Tunicamycin / Tunicamycin


Mass: 816.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H60N4O16 / Comment: antibiotic*YM
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 15 - 23 % (v/v) PEG 400, 100 mM Hepes pH 7.5 - 8.25, 4 % (v/v) aceton
PH range: 7.5 - 8.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→38.2 Å / Num. obs: 14664 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 62.66 Å2 / Net I/σ(I): 8.5
Reflection shellHighest resolution: 2.6 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J72

4j72


Resolution: 2.6→38.19 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.836 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.463 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.44 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.252 738 5.03 %RANDOM
Rwork0.226 ---
obs0.228 14664 70.9 %-
Displacement parametersBiso mean: 82 Å2
Baniso -1Baniso -2Baniso -3
1--2.7144 Å20 Å20 Å2
2---6.5159 Å20 Å2
3---9.2303 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 95 3 2440
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012496HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093383HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d823SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes359HARMONIC5
X-RAY DIFFRACTIONt_it2496HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.28
X-RAY DIFFRACTIONt_other_torsion20.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion354SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3020SEMIHARMONIC4
LS refinement shellHighest resolution: 2.6 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.203 -5.53 %
Rwork0.209 1059 -
obs--26.67 %
Refinement TLS params.Method: refined / Origin x: 166.193 Å / Origin y: 144.81 Å / Origin z: 261.738 Å
111213212223313233
T-0.538 Å20.092 Å2-0.066 Å2--0.5348 Å2-0.2439 Å2---0.2823 Å2
L6.4388 °20.384 °2-0.0296 °2-6.4955 °2-0.3295 °2--1.5281 °2
S0.289 Å °0.7642 Å °-1.299 Å °-0.8277 Å °-0.2928 Å °-0.0677 Å °0.3075 Å °-0.0296 Å °0.0038 Å °
Refinement TLS groupSelection details: { A|* }

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