[English] 日本語
Yorodumi
- PDB-5uxb: Crystal structure of macrolide 2'-phosphotransferase MphH from Br... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uxb
TitleCrystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium, apoenzyme
ComponentsMacrolide 2'-phosphotransferase MphH
KeywordsTRANSFERASE / 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
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / Predicted aminoglycoside phosphotransferase
Function and homology information
Biological speciesBrachybacterium faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsStogios, P.J. / Skarina, T. / 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 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 2.2Oct 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
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,6076
Polymers64,4652
Non-polymers1424
Water2,126118
1
A: Macrolide 2'-phosphotransferase MphH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2682
Polymers32,2321
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrolide 2'-phosphotransferase MphH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3394
Polymers32,2321
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.933, 79.741, 99.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Macrolide 2'-phosphotransferase MphH


Mass: 32232.416 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: C7MEP1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% PEG 400, 0.1 M HEPES pH 7.5, 1% trehalose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 25067 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rpim(I) all: 0.048 / Rsym value: 0.143 / Net I/σ(I): 16.28
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 3.78 / Num. unique obs: 771 / CC1/2: 0.962 / Rpim(I) all: 0.2 / Rsym value: 0.593 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UXC

5uxc


Resolution: 2.794→28.753 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1243 4.96 %RANDOM
Rwork0.2191 ---
obs0.2208 25067 87.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.794→28.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 4 118 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034581
X-RAY DIFFRACTIONf_angle_d0.5656272
X-RAY DIFFRACTIONf_dihedral_angle_d24.991613
X-RAY DIFFRACTIONf_chiral_restr0.04694
X-RAY DIFFRACTIONf_plane_restr0.004831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7941-2.90590.30641040.26421894X-RAY DIFFRACTION62
2.9059-3.0380.22681140.26332192X-RAY DIFFRACTION73
3.038-3.19790.27811230.25752446X-RAY DIFFRACTION80
3.1979-3.3980.24091430.23712561X-RAY DIFFRACTION85
3.398-3.65990.2551240.20722794X-RAY DIFFRACTION91
3.6599-4.02730.25221520.2052908X-RAY DIFFRACTION95
4.0273-4.6080.23151590.18893000X-RAY DIFFRACTION99
4.608-5.79780.23731600.21263041X-RAY DIFFRACTION100
5.7978-28.7550.27561640.22692988X-RAY DIFFRACTION99
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)
13.3316-1.705-1.2714.7099-3.01424.00650.4703-0.28020.61010.553-0.443-0.7856-0.3580.805-0.00080.7858-0.04790.08020.48940.02470.405427.98687.7938-16.9441
23.8693-1.299-2.08413.77320.01923.17670.27860.03620.1942-0.1654-0.101-0.3717-0.6773-0.0688-0.17310.5936-0.067-0.08180.3213-0.01290.282718.6086.0586-7.1591
30.62641.31390.20572.8994-0.77249.6103-0.42340.4583-0.3708-0.1164-0.1618-2.26320.91861.45970.52850.80710.03460.34880.4705-0.04311.299123.863525.90651.4018
41.37371.8782-0.80717.2690.37042.80580.112-0.07860.2318-0.3175-0.11441.09340.1171-0.36640.00960.2521-0.037-0.0820.35240.00720.35248.309113.51227.5101
53.0673-0.5691.22272.8697-0.71552.47660.1067-0.18110.1245-0.1395-0.0069-0.0620.0939-0.0217-0.10330.3506-0.011-0.02010.2689-0.03650.295819.904113.675117.3831
65.5926-1.0869-0.20741.1093-1.40464.8021-0.08590.81820.31940.0240.3067-0.9148-0.68870.4773-0.1990.419-0.0663-0.06140.3017-0.03670.4961-8.52127.894522.4428
71.6023-0.6632-1.08213.3018-0.26193.5673-0.23050.14110.1552-0.0827-0.1192-0.3075-0.0851-0.26520.36240.3678-0.0422-0.11410.2689-0.04540.3333-18.6346.008632.1619
86.3074-3.49850.60552.61340.96272.5570.27880.08920.5210.43240.0479-1.61430.12351.4704-0.34710.5152-0.0128-0.05480.54930.0350.9331-9.511222.794438.4539
91.24580.03510.27652.1001-0.92073.57380.0126-0.13180.0305-0.14070.02470.12370.0766-0.1951-0.02170.2390.03190.01780.213-0.04950.2881-22.392614.80154.2387
101.94451.85221.46137.67942.11993.07420.14810.0037-0.1138-1.14520.1496-0.8295-0.53510.6556-0.33250.3307-0.02940.16930.4380.04430.3866-1.678211.596259.5229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:31)
2X-RAY DIFFRACTION2(chain A and resid 32:96)
3X-RAY DIFFRACTION3(chain A and resid 97:113)
4X-RAY DIFFRACTION4(chain A and resid 114:144)
5X-RAY DIFFRACTION5(chain A and resid 145:298)
6X-RAY DIFFRACTION6(chain B and resid 2:31)
7X-RAY DIFFRACTION7(chain B and resid 32:96)
8X-RAY DIFFRACTION8(chain B and resid 97:106)
9X-RAY DIFFRACTION9(chain B and resid 107:266)
10X-RAY DIFFRACTION10(chain B and resid 267:298)

+
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