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- PDB-5uxd: Crystal structure of macrolide 2'-phosphotransferase MphH from Br... -

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Basic information

Entry
Database: PDB / ID: 5uxd
TitleCrystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium in complex with azithromycin
ComponentsMacrolide 2'-phosphotransferase MphH
KeywordsTRANSFERASE/ANTIBIOTIC / antibiotic resistance / macrolide / cave bacterium / phosphotransferase / kinase / alpha/beta protein / azithromycin / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID / TRANSFERASE-ANTIBIOTIC complex
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / AZITHROMYCIN / Predicted aminoglycoside phosphotransferase
Function and homology information
Biological speciesBrachybacterium faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStogios, P.J. / Skarina, T. / Wawrzak, Z. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: Nat Commun / Year: 2018
Title: The evolution of substrate discrimination in macrolide antibiotic resistance enzymes.
Authors: Pawlowski, A.C. / Stogios, P.J. / Koteva, K. / Skarina, T. / Evdokimova, E. / Savchenko, A. / Wright, G.D.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 21, 2018Group: Database references / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / pdbx_database_related
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 / _entity_poly.pdbx_target_identifier / _pdbx_database_related.db_id / _pdbx_database_related.db_name
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrolide 2'-phosphotransferase MphH
B: Macrolide 2'-phosphotransferase MphH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,07813
Polymers64,4262
Non-polymers2,65211
Water22,4651247
1
A: Macrolide 2'-phosphotransferase MphH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9498
Polymers32,2131
Non-polymers1,7367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrolide 2'-phosphotransferase MphH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1295
Polymers32,2131
Non-polymers9164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.050, 81.210, 71.340
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Macrolide 2'-phosphotransferase MphH


Mass: 32213.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / NCIB 9860) (bacteria)
Strain: ATCC 43885 / DSM 4810 / NCIB 9860 / Gene: Bfae_22410 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: C7MEP1
#2: Chemical ChemComp-ZIT / AZITHROMYCIN


Mass: 748.984 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H72N2O12 / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2 M ammonium sulfate, 5 mM azithromycin, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→45.345 Å / Num. obs: 67267 / % possible obs: 98.1 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Rsym value: 0.086 / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5045 / CC1/2: 0.706 / Rpim(I) all: 0.417 / Rsym value: 0.845 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UXC

5uxc


Resolution: 1.7→45.345 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2000 2.98 %RANDOM
Rwork0.1905 ---
obs0.1918 67224 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 172 1247 5951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064930
X-RAY DIFFRACTIONf_angle_d0.946798
X-RAY DIFFRACTIONf_dihedral_angle_d3.8533794
X-RAY DIFFRACTIONf_chiral_restr0.056778
X-RAY DIFFRACTIONf_plane_restr0.008873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.33611450.2944736X-RAY DIFFRACTION100
1.7207-1.74250.3351420.2894610X-RAY DIFFRACTION100
1.7425-1.76540.32711430.28014713X-RAY DIFFRACTION100
1.7654-1.78960.36651430.27164625X-RAY DIFFRACTION100
1.7896-1.81520.29081420.25264633X-RAY DIFFRACTION100
1.8152-1.84230.24351490.25264762X-RAY DIFFRACTION100
1.8423-1.87110.29071390.25864605X-RAY DIFFRACTION100
1.8711-1.90180.39911280.33124111X-RAY DIFFRACTION87
1.9018-1.93460.48631280.44094131X-RAY DIFFRACTION89
1.9346-1.96970.38141310.33674235X-RAY DIFFRACTION90
1.9697-2.00760.32881430.23094627X-RAY DIFFRACTION100
2.0076-2.04860.25471450.20684700X-RAY DIFFRACTION100
2.0486-2.09310.22581440.19064688X-RAY DIFFRACTION100
2.0931-2.14180.28331420.19544643X-RAY DIFFRACTION100
2.1418-2.19540.23661460.19844695X-RAY DIFFRACTION100
2.1954-2.25470.34481250.29824124X-RAY DIFFRACTION88
2.2547-2.32110.3261340.25654288X-RAY DIFFRACTION91
2.3211-2.3960.24681440.19834672X-RAY DIFFRACTION100
2.396-2.48160.25131410.18534606X-RAY DIFFRACTION100
2.4816-2.5810.26111440.17364737X-RAY DIFFRACTION100
2.581-2.69840.20631410.17244639X-RAY DIFFRACTION100
2.6984-2.84070.19391430.17094676X-RAY DIFFRACTION100
2.8407-3.01860.24111430.17034683X-RAY DIFFRACTION100
3.0186-3.25160.1861440.164705X-RAY DIFFRACTION100
3.2516-3.57870.16681430.14174651X-RAY DIFFRACTION100
3.5787-4.09630.17541400.13724651X-RAY DIFFRACTION99
4.0963-5.15980.15471450.13284677X-RAY DIFFRACTION100
5.1598-45.36120.18211410.15574655X-RAY DIFFRACTION100

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