[English] 日本語
Yorodumi
- PDB-8ot2: Structural and functional studies of geldanamycin amide synthase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ot2
TitleStructural and functional studies of geldanamycin amide synthase ShGdmF
ComponentsGdmF
KeywordsBIOSYNTHETIC PROTEIN / amide synthase / geldanamycin / amidase / alpha-beta
Function / homology: / Arylamine N-acetyltransferase / N-acetyltransferase / arylamine N-acetyltransferase activity / Papain-like cysteine peptidase superfamily / ACETATE ION / DI(HYDROXYETHYL)ETHER / : / GdmF
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsEwert, W. / Zeilinger, C. / Kirschning, A. / Preller, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Structural and functional studies of geldanamycin amide synthase ShGdmF
Authors: Ewert, W. / Bartens, C. / Heutling, A. / Ongouta, J. / Vogt, M. / Kishore, A. / Zeilinger, C. / Preller, M.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GdmF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,11119
Polymers29,8381
Non-polymers1,27218
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-3 kcal/mol
Surface area11570 Å2
Unit cell
Length a, b, c (Å)72.544, 96.390, 86.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein GdmF


Mass: 29838.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmF / Production host: Escherichia coli (E. coli) / References: UniProt: Q84G21

-
Non-polymers , 6 types, 85 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-W0E / 3-azanyl-5-methyl-phenol


Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 25 % PEG4000, 150 mM Sodium acetate, 200 mM lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→42.12 Å / Num. obs: 29337 / % possible obs: 97.94 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0769 / Net I/σ(I): 21.26
Reflection shellResolution: 1.77→1.833 Å / Rmerge(I) obs: 1.358 / Num. unique obs: 2867 / CC1/2: 0.694 / % possible all: 96.86

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→42.12 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1848 1477 5.04 %
Rwork0.1698 27852 -
obs0.1705 29329 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.64 Å2
Refinement stepCycle: LAST / Resolution: 1.77→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 82 67 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022021
X-RAY DIFFRACTIONf_angle_d1.12552726
X-RAY DIFFRACTIONf_chiral_restr0.0643290
X-RAY DIFFRACTIONf_plane_restr0.0072358
X-RAY DIFFRACTIONf_dihedral_angle_d26.9545294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.29171310.2482465X-RAY DIFFRACTION96.83
1.83-1.890.26911330.21392467X-RAY DIFFRACTION96.69
1.89-1.970.20141190.17472484X-RAY DIFFRACTION97.16
1.97-2.060.18631250.15872487X-RAY DIFFRACTION97.35
2.06-2.170.18711330.1522510X-RAY DIFFRACTION97.53
2.17-2.30.15691180.14622540X-RAY DIFFRACTION98.15
2.3-2.480.17841380.14892510X-RAY DIFFRACTION98
2.48-2.730.16971630.15232518X-RAY DIFFRACTION98.57
2.73-3.120.18511540.14892549X-RAY DIFFRACTION98.9
3.12-3.940.14811250.15322607X-RAY DIFFRACTION99.06
3.94-42.120.20221380.19962715X-RAY DIFFRACTION99.2

+
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