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- PDB-5uxa: Crystal structure of macrolide 2'-phosphotransferase MphB from Es... -

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Basic information

Entry
Database: PDB / ID: 5uxa
TitleCrystal structure of macrolide 2'-phosphotransferase MphB from Escherichia coli
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE / antibiotic resistance / macrolide / phosphotransferase / kinase / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / Macrolide 2'-phosphotransferase II
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Evdokimova, E. / Egorova, O. / Di Leo, R. / 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 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrolide 2'-phosphotransferase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6474
Polymers34,5271
Non-polymers1203
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area16690 Å2
MethodPISA
2
A: Macrolide 2'-phosphotransferase II
hetero molecules

A: Macrolide 2'-phosphotransferase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2958
Polymers69,0542
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5880 Å2
ΔGint-55 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.276, 116.684, 92.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-622-

HOH

31A-754-

HOH

41A-813-

HOH

51A-851-

HOH

61A-891-

HOH

71A-943-

HOH

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Components

#1: Protein Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B)


Mass: 34527.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mphB, pO103_99 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 18% PEG 8K

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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 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 27167 / % possible obs: 100 % / Redundancy: 8.6 % / Rpim(I) all: 0.033 / Rsym value: 0.092 / Net I/σ(I): 24.94
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1354 / CC1/2: 0.905 / Rpim(I) all: 0.282 / Rsym value: 0.793 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→29.171 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1916 7.34 %RANDOM
Rwork0.1513 ---
obs0.155 26109 95.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 3 450 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162501
X-RAY DIFFRACTIONf_angle_d1.1563396
X-RAY DIFFRACTIONf_dihedral_angle_d18.48920
X-RAY DIFFRACTIONf_chiral_restr0.083367
X-RAY DIFFRACTIONf_plane_restr0.008439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9421-1.99070.25861140.18911473X-RAY DIFFRACTION83
1.9907-2.04450.21581270.18891630X-RAY DIFFRACTION90
2.0445-2.10460.25431290.17031621X-RAY DIFFRACTION92
2.1046-2.17250.23431250.17091673X-RAY DIFFRACTION94
2.1725-2.25010.19021300.15921711X-RAY DIFFRACTION95
2.2501-2.34020.23191410.14981709X-RAY DIFFRACTION96
2.3402-2.44670.24551360.16121731X-RAY DIFFRACTION97
2.4467-2.57560.20891430.15671747X-RAY DIFFRACTION98
2.5756-2.73680.20911370.15931763X-RAY DIFFRACTION98
2.7368-2.9480.24411460.16261778X-RAY DIFFRACTION99
2.948-3.24430.20811380.14961806X-RAY DIFFRACTION99
3.2443-3.71290.17251460.12861829X-RAY DIFFRACTION100
3.7129-4.67480.14411440.12531818X-RAY DIFFRACTION100
4.6748-29.17430.2111600.16311904X-RAY DIFFRACTION100
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)
15.01274.1236-2.67644.7008-2.92972.5297-0.40230.61880.8094-1.1840.39220.235-0.1176-0.1813-0.09771.2764-0.2468-0.30610.48040.21481.202639.488764.756733.1404
24.7083-6.6-1.5549.43480.98868.2870.49441.4690.937-1.1794-0.616-0.1414-0.035-0.72820.06640.9279-0.2468-0.17510.88930.28310.842640.548155.899831.2764
34.5675-0.6738-1.91735.2418-0.18034.48610.02870.5450.9237-0.3718-0.02920.2051-0.9566-0.09870.0040.4279-0.0336-0.12090.230.04010.395233.613950.255139.9285
45.63932.7001-2.0744.61613.23177.2431-0.12360.55450.3494-0.52940.1497-0.0414-0.55110.0449-0.02050.21340.027-0.0280.36320.02670.223942.055333.1524.5216
52.63540.1035-0.0890.89490.10631.6979-0.01910.13230.0404-0.0394-0.00810.07930.0038-0.09170.03010.13860.00950.00960.126-0.00820.151421.47528.392934.7867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:15)
2X-RAY DIFFRACTION2(chain A and resid 16:32)
3X-RAY DIFFRACTION3(chain A and resid 33:94)
4X-RAY DIFFRACTION4(chain A and resid 95:121)
5X-RAY DIFFRACTION5(chain A and resid 122:302)

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