[English] 日本語
Yorodumi
- PDB-5igy: Macrolide 2'-phosphotransferase type II - complex with GDP and er... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5igy
TitleMacrolide 2'-phosphotransferase type II - complex with GDP and erythromycin
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE / macrolide phosphotransferase / kinase
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / ERYTHROMYCIN A / GUANOSINE-5'-DIPHOSPHATE / Macrolide 2'-phosphotransferase II
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,7444
Polymers34,5271
Non-polymers1,2173
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.870, 80.520, 97.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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) / Strain: BM2506 / Gene: mphB, pO103_99 / Plasmid: pET28a / 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→41.818 Å / Num. obs: 56698 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.55
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.490.7582.85199.9
1.49-1.530.5613.81100
1.53-1.570.4185.15199.9
1.57-1.620.3256.621100
1.62-1.670.2688.181100
1.67-1.730.20310.661100
1.73-1.80.15913.351100
1.8-1.870.1217.411100
1.87-1.960.08623.881100
1.96-2.050.06829.591100
2.05-2.160.05535.95199.9
2.16-2.290.04841.041100
2.29-2.450.04344.571100
2.45-2.650.03848.841100
2.65-2.90.03553.891100
2.9-3.240.03158.621100
3.24-3.740.02962.36199.9
3.74-4.590.02764.71199.9
4.59-6.480.02663.71100
6.480.02861.08198.2

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5IGW

5igw


Resolution: 1.45→41.818 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.3
RfactorNum. reflection% reflection
Rfree0.1958 2835 5 %
Rwork0.1701 --
obs0.1714 56698 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.79 Å2 / Biso mean: 20.84 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 1.45→41.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 159 520 3061
Biso mean--12.33 30.05 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092589
X-RAY DIFFRACTIONf_angle_d1.3023535
X-RAY DIFFRACTIONf_chiral_restr0.064386
X-RAY DIFFRACTIONf_plane_restr0.006444
X-RAY DIFFRACTIONf_dihedral_angle_d14.365936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4499-1.47490.26391400.251226602800
1.4749-1.50170.26981380.243726132751
1.5017-1.53060.24551410.222526922833
1.5306-1.56180.23981380.206526102748
1.5618-1.59580.25841430.198827052848
1.5958-1.63290.2351380.1926312769
1.6329-1.67380.23471400.184326602800
1.6738-1.7190.26531410.178426822823
1.719-1.76960.20021400.183626592799
1.7696-1.82670.21751420.179426832825
1.8267-1.8920.22451410.1826862827
1.892-1.96780.24091390.173526572796
1.9678-2.05730.21361420.168626852827
2.0573-2.16580.16431400.157826852825
2.1658-2.30150.18521430.152127102853
2.3015-2.47910.16131420.155227092851
2.4791-2.72860.16741440.159527182862
2.7286-3.12330.21440.16227442888
3.1233-3.93460.16011470.151827792926
3.9346-41.83540.18931520.172228953047
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)
13.2336-0.24850.08031.82480.26442.04090.2253-0.2016-0.7610.24880.005-0.00510.4622-0.048-0.25830.48350.0211-0.22580.22230.01010.34911.5774-10.960151.0584
23.18013.29064.78533.9615.69888.5830.1129-0.28120.00540.5008-0.12120.1622-0.0422-0.1840.0270.3536-0.07110.0220.2524-0.00170.17770.4551-7.43949.5316
30.9951.06430.93383.07242.60343.030.0694-0.147-0.16060.2109-0.1006-0.07710.1533-0.23080.08420.21740.0238-0.06020.1827-0.0350.15755.3438-6.209943.7404
45.89251.0805-1.50252.7407-0.50922.52830.08180.041-0.1968-0.13040.1665-0.3080.1030.2001-0.11440.3917-0.0335-0.11950.1731-0.08850.5098.0469-20.626335.6561
51.1683-0.78712.1475.9173-2.22894.0611-0.0847-0.07-0.3308-0.0107-0.0956-0.30570.56520.21140.1420.28280.0896-0.00970.2449-0.01880.280812.9105-14.896729.5888
60.8555-0.25630.07120.93220.31430.7422-0.01010.07750.1588-0.00970.1678-0.30230.00110.36660.07610.0540.0226-0.04550.1673-0.05780.201310.63070.689727.9872
72.38990.43021.2050.36720.85091.9970.15150.0131-0.37330.14850.059-0.18380.31110.101-0.21910.20290.0862-0.1810.1905-0.09380.341614.1416-10.331738.8434
82.4763-0.54051.38861.35160.78692.0165-0.1199-0.2759-0.13080.28640.09390.07830.1406-0.15330.03040.10640.0157-0.00160.1109-0.00760.0762-2.9083-3.675637.5052
94.6381-2.64890.44054.9360.18744.2394-0.1895-0.369-0.0930.146-0.05540.41110.0818-0.26660.17760.09090.0350.01910.2288-0.03480.1665-16.4769-0.045232.5015
104.3287-1.2875-0.82161.31270.22321.4013-0.05810.10390.37-0.040.0762-0.1413-0.26110.0976-0.02830.067-0.0242-0.02410.0863-0.00080.12172.51624.989721.1842
114.3514-1.14520.54334.1082-1.98223.19740.01080.1545-0.0141-0.18490.1428-0.33150.14550.2381-0.08890.13920.01290.05920.1464-0.05030.11189.2659-9.392712.9674
120.78710.1219-0.0731.2538-0.00551.0247-0.06470.2506-0.3006-0.2027-0.0190.03370.4124-0.1393-0.0080.3512-0.07130.05970.1475-0.09010.1367-1.7982-17.43258.6758
130.2758-0.51620.02971.6829-0.51380.29880.07140.0819-0.3459-0.1341-0.07720.28850.4234-0.2714-0.23310.3495-0.2632-0.04240.2766-0.20880.1651-12.0594-18.11238.0629
143.21791.30011.88842.09421.5261.9264-0.16980.3970.1213-0.4945-0.08930.0534-0.1154-0.14920.13990.2633-0.03150.02770.2681-0.00120.0749-3.7196-4.56183.1017
151.04290.0524-0.00720.7897-0.24961.2556-0.1243-0.02530.14760.04360.0446-0.00280.0256-0.1340.05940.04610.005-0.01470.0719-0.01890.0762-3.1044-1.553324.667
164.26690.5352-0.76251.70040.35451.6445-0.08720.25140.3149-0.1920.09790.2167-0.2018-0.19130.05510.0762-0.0076-0.0450.10810.04270.1449-8.0997.503115.686
175.83722.5916-1.17154.1474-0.85522.63760.06850.48420.2183-0.46060.03780.0905-0.1992-0.2796-0.0510.18150.0004-0.01650.16450.03830.1063-6.24942.42447.6809
180.71450.1477-0.67420.48570.12081.4008-0.1730.1304-0.19870.0368-0.0230.0920.4786-0.2160.10960.1922-0.08280.01920.1353-0.03060.1181-9.0183-12.320616.368
193.9073-2.35571.8433.03881.06233.795-0.2441-0.4073-0.28730.10210.01660.28490.3699-0.34240.15040.32580.00680.0970.19340.0490.3304-9.7853-22.828426.6354
207.46192.84251.47976.4495-2.55434.00640.0668-0.1280.1570.17050.02510.50620.011-0.2205-0.09860.4534-0.29540.21250.5347-0.16050.6225-17.1612-21.456917.8578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:19)A4 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:29)A20 - 29
3X-RAY DIFFRACTION3(chain A and resid 30:51)A30 - 51
4X-RAY DIFFRACTION4(chain A and resid 52:56)A52 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:62)A57 - 62
6X-RAY DIFFRACTION6(chain A and resid 63:81)A63 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:89)A82 - 89
8X-RAY DIFFRACTION8(chain A and resid 90:106)A90 - 106
9X-RAY DIFFRACTION9(chain A and resid 107:118)A107 - 118
10X-RAY DIFFRACTION10(chain A and resid 119:144)A119 - 144
11X-RAY DIFFRACTION11(chain A and resid 145:153)A145 - 153
12X-RAY DIFFRACTION12(chain A and resid 154:168)A154 - 168
13X-RAY DIFFRACTION13(chain A and resid 169:184)A169 - 184
14X-RAY DIFFRACTION14(chain A and resid 185:193)A185 - 193
15X-RAY DIFFRACTION15(chain A and resid 194:240)A194 - 240
16X-RAY DIFFRACTION16(chain A and resid 241:256)A241 - 256
17X-RAY DIFFRACTION17(chain A and resid 257:264)A257 - 264
18X-RAY DIFFRACTION18(chain A and resid 265:280)A265 - 280
19X-RAY DIFFRACTION19(chain A and resid 281:293)A281 - 293
20X-RAY DIFFRACTION20(chain A and resid 294:298)A294 - 298

+
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://pdbjlvh1.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