[English] 日本語
Yorodumi
- PDB-3d40: Crystal structure of fosfomycin resistance kinase FomA from Strep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d40
TitleCrystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with diphosphate
ComponentsFomA protein
KeywordsTRANSFERASE / fosfomycin / antibiotic resistance / kinase / phosphoryl transfer
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / Newcomer, M.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.
Authors: Pakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / Newcomer, M.E.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0512
Polymers30,8771
Non-polymers1741
Water4,161231
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1024
Polymers61,7542
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area3380 Å2
ΔGint-17.1 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.361, 88.361, 79.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein FomA protein


Mass: 30876.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wedmorensis (bacteria) / Gene: fomA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56187
#2: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE RESEQUENCING OF THE PROTEIN CONFIRMED RESIDUE 31 IS ARG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38079 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. all: 52986 / Num. obs: 52986 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.04 / Net I/σ(I): 34.8
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4585 / Rsym value: 0.51 / % possible all: 85.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model of SeMet FomA form based on MAD data

Resolution: 1.53→27.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.221 / SU ML: 0.04 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19801 834 1.6 %RANDOM
Rwork0.16864 ---
all0.16908 50201 --
obs0.16908 50201 94.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 9 231 2193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222001
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9712716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4095250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.621.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6711522
X-RAY DIFFRACTIONr_chiral_restr0.1230.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021501
X-RAY DIFFRACTIONr_nbd_refined0.2110.2920
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.221
X-RAY DIFFRACTIONr_mcbond_it1.251.51288
X-RAY DIFFRACTIONr_mcangle_it1.91722019
X-RAY DIFFRACTIONr_scbond_it2.8033793
X-RAY DIFFRACTIONr_scangle_it4.4184.5697
LS refinement shellHighest resolution: 1.53 Å / Num. reflection Rwork: 2784 / Total num. of bins used: 20

+
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