[English] 日本語
Yorodumi
- PDB-8px4: Structure of the PAS domain code by the LIC_11128 gene from Lepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8px4
TitleStructure of the PAS domain code by the LIC_11128 gene from Leptospira interrogans serovar Copenhageni Fiocruz, solved at wavelength 3.09 A
ComponentsDiguanylate cyclase
KeywordsUNKNOWN FUNCTION / GGDEF family protein
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Guzzo, C.R. / Owens, R.J. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diguanylate cyclase
B: Diguanylate cyclase
C: Diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)40,3233
Polymers40,3233
Non-polymers00
Water1267
1
A: Diguanylate cyclase
C: Diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)26,8822
Polymers26,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-17 kcal/mol
Surface area10960 Å2
MethodPISA
2
B: Diguanylate cyclase

B: Diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)26,8822
Polymers26,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2140 Å2
ΔGint-16 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 144.560, 48.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Diguanylate cyclase


Mass: 13441.053 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Gene: FVE87_03295 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G9EEG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-Tris pH 5,5, 17% w/v PEG 10,000, and 0.1 M Ammonium acetate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.09 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.09 Å / Relative weight: 1
ReflectionResolution: 2.5→72.28 Å / Num. obs: 12470 / % possible obs: 81.04 % / Redundancy: 49.2 % / Biso Wilson estimate: 64.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08298 / Rpim(I) all: 0.0117 / Rrim(I) all: 0.08386 / Net I/σ(I): 41.69
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.433 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 1065 / CC1/2: 0.636 / % possible all: 78.66

-
Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→72.28 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.063 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 2.951 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27653 549 4.8 %RANDOM
Rwork0.24152 ---
obs0.24325 10829 81.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.629 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å2-0 Å2
2--0.43 Å2-0 Å2
3---1.35 Å2
Refinement stepCycle: 1 / Resolution: 2.5→72.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 7 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122732
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162552
X-RAY DIFFRACTIONr_angle_refined_deg0.6561.653701
X-RAY DIFFRACTIONr_angle_other_deg0.2431.5765860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.063521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47310461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0360.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8985.5051297
X-RAY DIFFRACTIONr_mcbond_other3.8975.5041297
X-RAY DIFFRACTIONr_mcangle_it5.5439.91616
X-RAY DIFFRACTIONr_mcangle_other5.5439.9011617
X-RAY DIFFRACTIONr_scbond_it5.4826.4271435
X-RAY DIFFRACTIONr_scbond_other5.486.4271436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.67311.4382086
X-RAY DIFFRACTIONr_long_range_B_refined10.62355.922788
X-RAY DIFFRACTIONr_long_range_B_other10.62155.922789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 32 -
Rwork0.294 756 -
obs--78.8 %
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)
10.78790.19710.24181.0123-0.80092.52970.0335-0.0276-0.03590.17110.18430.0796-0.1727-0.047-0.21780.12780.05520.02590.0710.01910.024526.309726.939741.5317
23.1619-1.12930.09532.4882-0.70670.2260.0072-0.0753-0.4736-0.09210.0430.35550.01220.0116-0.05020.0656-0.0449-0.02330.04420.05440.215711.1492-5.020832.6695
30.0460.02830.37263.3460.44463.0783-0.02710.0074-0.0286-0.24920.27710.1843-0.13020.0593-0.250.1071-0.0239-0.01350.07310.05850.075518.789521.571319.2605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 116
2X-RAY DIFFRACTION2B10 - 116
3X-RAY DIFFRACTION3C9 - 116

+
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