[English] 日本語
Yorodumi
- PDB-5igi: Macrolide 2'-phosphotransferase type I - complex with guanosine a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5igi
TitleMacrolide 2'-phosphotransferase type I - complex with guanosine and azithromycin
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE-ANTIBIOTIC complex
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / GUANOSINE / ISOPROPYL ALCOHOL / AZITHROMYCIN / Macrolide 2'-phosphotransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsBerghuis, A.M. / Fong, D.H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-13107 Canada
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.
Authors: Fong, D.H. / Burk, D.L. / Blanchet, J. / Yan, A.Y. / Berghuis, A.M.
History
DepositionFeb 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3594
Polymers33,2671
Non-polymers1,0923
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Macrolide 2'-phosphotransferase
hetero molecules

A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7188
Polymers66,5342
Non-polymers2,1856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area5930 Å2
ΔGint-30 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.310, 45.310, 247.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Macrolide 2'-phosphotransferase / Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'- ...Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'-phosphotransferase Mph(A) / Macrolide 2-phosphotransferase / Macrolide 2-phosphotransferase protein / macrolide resistance protein / Macrolide-phosphotransferase / mph(A) / Mph(A) / Mph(A) macrolide 2'-phosphotransferase I / Uncharacterized protein


Mass: 33266.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Tf481A
Gene: mphA, mph(A), mph2, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, ...Gene: mphA, mph(A), mph2, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, orf00017, pCTXM123_C0996_11, pKC394-009, SK74_04859, SK86_03516, UN86_19875
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47396
#2: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical ChemComp-ZIT / AZITHROMYCIN / Azithromycin


Mass: 748.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H72N2O12 / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2 / Details: 0.1 M Na citrate, 25% PEG 4000, 17% isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→39.24 Å / Num. obs: 90023 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.51
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.2-1.230.2432.95171.6
1.23-1.260.2263.63182.6
1.26-1.30.2124.36192.6
1.3-1.340.1795.89198.7
1.34-1.390.1568.271100
1.39-1.430.13210.62199.9
1.43-1.490.10612.98199.9
1.49-1.550.08815.52199.9
1.55-1.620.07418.19199.9
1.62-1.70.06520.3199.7
1.7-1.790.05623.47199.9
1.79-1.90.04926.49199.5
1.9-2.030.04330.18199.6
2.03-2.190.0433.22199.3
2.19-2.40.03935.07198.9
2.4-2.680.03736.29199
2.68-3.10.03538.46199
3.1-3.790.03439.81198.1
3.79-5.370.03439.68197.6
5.370.03537.84192.7

-
Processing

Software
NameVersionClassification
XDSMarch 5, 2012data reduction
XSCALEdata scaling
PHENIX1.8_1069phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5IGH

5igh


Resolution: 1.2→39.24 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.34
RfactorNum. reflection% reflection
Rfree0.1628 4515 5.02 %
Rwork0.1608 --
obs0.1609 90019 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.53 Å2 / Biso mean: 18.88 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 1.2→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 172 506 3012
Biso mean--17.42 29.14 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012618
X-RAY DIFFRACTIONf_angle_d1.4013605
X-RAY DIFFRACTIONf_chiral_restr0.088417
X-RAY DIFFRACTIONf_plane_restr0.007461
X-RAY DIFFRACTIONf_dihedral_angle_d11.932926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.19361090.21841971208068
1.2136-1.22790.20971060.21262231233774
1.2279-1.24290.23261260.20732234236078
1.2429-1.25860.21131360.22462498263484
1.2586-1.27520.25551350.24422538267388
1.2752-1.29260.26121470.2272757290493
1.2926-1.31110.2171450.21012813295896
1.3111-1.33070.20461570.18582940309799
1.3307-1.35150.20511480.177129113059100
1.3515-1.37360.17091610.176729643125100
1.3736-1.39730.18491530.176928943047100
1.3973-1.42270.19751550.17429753130100
1.4227-1.45010.2281540.177829203074100
1.4501-1.47970.19131520.170229563108100
1.4797-1.51190.2081590.171129833142100
1.5119-1.5470.181510.159829053056100
1.547-1.58570.16361570.152929453102100
1.5857-1.62860.17051590.152529853144100
1.6286-1.67650.16471550.153829743129100
1.6765-1.73060.15821550.158329453100100
1.7306-1.79250.16451600.161929733133100
1.7925-1.86420.16031570.15932951310899
1.8642-1.94910.17831600.154229763136100
1.9491-2.05180.16531570.15152994315199
2.0518-2.18040.13421630.14343018318199
2.1804-2.34870.17681550.14742955311099
2.3487-2.5850.15371590.15212988314799
2.585-2.9590.16591550.16093056321199
2.959-3.72760.13451590.15293082324198
3.7276-39.26060.15881700.16853172334296
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)
15.1234-2.91522.08072.5271-1.84541.40150.1447-0.30840.4442-0.4763-0.09670.2385-0.6410.1597-0.12290.4177-0.0966-0.02330.2339-0.01690.318334.735357.2644290.1087
21.71110.256-0.05972.391-1.46273.0430.1665-0.1270.19160.42810.00140.1785-0.6228-0.3013-0.16520.32970.05710.01190.1618-0.01120.163423.682958.6357283.0918
33.5081-2.67250.45034.56182.60243.5255-0.2574-0.44240.04390.37610.0981-0.1697-0.0948-0.2410.17590.24550.0196-0.03750.4106-0.0330.221531.258848.0743286.0261
40.55780.9758-0.21422.0387-1.24312.6134-0.0689-0.0009-0.1360.1336-0.0711-0.08420.00320.05880.10250.16920.00650.00840.17360.00340.165928.574650.0364279.2848
52.90951.88631.0591.73130.68520.70010.00490.26330.016-0.04380.03970.0142-0.05330.1068-0.0360.11720.01340.00150.1172-0.00240.118526.532849.2517263.6948
63.5042-1.06631.13796.2904-3.30183.7660.1299-0.08480.27790.3513-0.07870.5849-0.2822-0.685-0.06730.19050.0302-0.00310.4218-0.04940.210813.687238.8354264.1511
70.47760.2516-0.36511.06110.14810.65860.0137-0.04070.0660.0894-0.01870.097-0.0258-0.0487-0.00580.10970.0109-0.00270.1253-0.00210.119221.982845.8048275.1292
87.20111.08670.16832.2075-0.34732.8729-0.0155-0.38090.74810.0389-0.0816-0.1179-0.00760.30730.10290.18130.0187-0.01020.197-0.00960.180333.734930.0241282.3349
90.6299-0.1424-0.00640.46250.27980.9140.02730.0556-0.02830.0017-0.05740.01970.0638-0.04810.02360.0711-0.002-0.00550.09720.00320.08723.910332.7519259.5057
104.05990.9342.04910.93680.29451.08-0.04720.290.2799-0.0248-0.2196-0.2896-0.21560.7370.11850.097-0.0202-0.00990.26660.07420.169147.628637.2593255.45
112.05490.77491.20360.41620.49411.31910.07120.2522-0.2052-0.01440.0777-0.29420.10760.3946-0.10670.09260.01520.00840.1446-0.01710.150549.258225.8403255.8344
120.7043-0.0284-0.16150.73470.21250.6858-0.0164-0.0097-0.06320.0464-0.00690.00620.04230.03650.02680.0759-0.0027-0.00340.10010.00260.089628.467130.6265.1553
136.3574-0.70332.41652.4378-0.48893.2861-0.04-0.4649-0.60750.08130.0951-0.27390.317-0.0377-0.01780.13280.0030.02110.15030.04710.231827.123916.9796266.315
141.86440.2761-0.39120.3965-0.10410.56720.01610.01880.0719-0.0291-0.01070.01220.00340.0347-0.00370.09410.0080.00120.10550.0010.114634.853327.8143260.3392
151.7855-0.3556-0.03592.70150.27172.37450.08-0.42840.18950.239-0.020.0402-0.0824-0.0084-0.04870.1349-0.0231-0.01110.2535-0.02220.18251.282435.1344269.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:11)A2 - 11
2X-RAY DIFFRACTION2(chain A and resid 12:26)A12 - 26
3X-RAY DIFFRACTION3(chain A and resid 27:30)A27 - 30
4X-RAY DIFFRACTION4(chain A and resid 31:56)A31 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:73)A57 - 73
6X-RAY DIFFRACTION6(chain A and resid 74:78)A74 - 78
7X-RAY DIFFRACTION7(chain A and resid 79:102)A79 - 102
8X-RAY DIFFRACTION8(chain A and resid 103:118)A103 - 118
9X-RAY DIFFRACTION9(chain A and resid 119:157)A119 - 157
10X-RAY DIFFRACTION10(chain A and resid 158:170)A158 - 170
11X-RAY DIFFRACTION11(chain A and resid 171:185)A171 - 185
12X-RAY DIFFRACTION12(chain A and resid 186:240)A186 - 240
13X-RAY DIFFRACTION13(chain A and resid 241:249)A241 - 249
14X-RAY DIFFRACTION14(chain A and resid 250:284)A250 - 284
15X-RAY DIFFRACTION15(chain A and resid 285:301)A285 - 301

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more