[English] 日本語
Yorodumi
- PDB-6bde: Crystal structure of Fe(II) unliganded H-NOX protein mutant A71G ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bde
TitleCrystal structure of Fe(II) unliganded H-NOX protein mutant A71G from K. algicida
Components2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
KeywordsSIGNALING PROTEIN / Nitric oxide signaling / heme nitric oxide/oxygen sensing protein
Function / homologyHeme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Function and homology information
Biological speciesKordia algicida OT-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å
AuthorsBruegger, J.J. / Hespen, C.W. / Marletta, M.A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins.
Authors: Hespen, C.W. / Bruegger, J.J. / Guo, Y. / Marletta, M.A.
History
DepositionOct 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8872
Polymers21,2701
Non-polymers6161
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.794, 56.730, 68.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase


Mass: 21270.156 Da / Num. of mol.: 1 / Mutation: A71G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kordia algicida OT-1 (bacteria) / Gene: KAOT1_17313 / Production host: Escherichia coli (E. coli) / References: UniProt: A9DSJ8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.24 Å3/Da / Density % sol: 45.01 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 0.3 M LiCl, 34% PEG 6000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 23704 / % possible obs: 99.5 % / Redundancy: 12.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Χ2: 1.009 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.688.30.5311330.950.1860.5640.94896.3
1.68-1.719.80.50111580.9550.1670.531.0199.8
1.71-1.7411.30.47911780.9690.1480.5021.005100
1.74-1.78120.4111490.9740.1240.4281.051100
1.78-1.8212.10.3411930.9830.1030.3561.01599.9
1.82-1.8612.20.2911470.9880.0870.3031.011100
1.86-1.912.30.23411800.9920.0690.2441.01399.9
1.9-1.9612.70.20311900.9910.0590.2121.014100
1.96-2.0112.90.17511630.9930.050.1821.008100
2.01-2.0813.20.15611780.9930.0440.1621.04299.8
2.08-2.1512.90.14111740.9950.0410.1471.007100
2.15-2.2412.50.12911830.9950.0380.1340.955100
2.24-2.3412.90.11811920.9930.0340.1231.00599.9
2.34-2.4612.80.11111750.9960.0320.1160.96100
2.46-2.6213.30.10112060.9950.0290.1051.052100
2.62-2.8212.90.09411940.9970.0270.0981.038100
2.82-3.1112.40.08911960.9960.0260.0931.01199.7
3.11-3.5512.90.0812130.9960.0230.0831.03199.4
3.55-4.48120.07411980.9960.0220.0771.04296.9
4.48-5011.70.06713040.9970.0210.070.94298.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDD

6bdd


Resolution: 1.641→39.791 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.54
RfactorNum. reflection% reflection
Rfree0.2362 1183 5.01 %
Rwork0.2103 --
obs0.2117 23631 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.22 Å2 / Biso mean: 47.4573 Å2 / Biso min: 24.72 Å2
Refinement stepCycle: final / Resolution: 1.641→39.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 43 126 1664
Biso mean--35.95 52.05 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051575
X-RAY DIFFRACTIONf_angle_d2.8162139
X-RAY DIFFRACTIONf_chiral_restr0.04235
X-RAY DIFFRACTIONf_plane_restr0.003267
X-RAY DIFFRACTIONf_dihedral_angle_d6.256933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6412-1.71590.35731460.28642539268591
1.7159-1.80640.28611350.264927892924100
1.8064-1.91960.31011420.253428212963100
1.9196-2.06780.27461510.233327972948100
2.0678-2.27580.23191540.227628322986100
2.2758-2.60510.24631270.225728652992100
2.6051-3.28190.27931630.230428613024100
3.2819-39.80310.21650.18212944310998
Refinement TLS params.Method: refined / Origin x: 2.6513 Å / Origin y: -6.7623 Å / Origin z: -1.8656 Å
111213212223313233
T0.2267 Å2-0.0257 Å2-0.048 Å2-0.2843 Å20.0248 Å2--0.2305 Å2
L4.3661 °2-0.0623 °20.1251 °2-1.7139 °20.2128 °2--2.4037 °2
S-0.1545 Å °0.3779 Å °0.2852 Å °-0.0619 Å °-0.074 Å °0.1034 Å °-0.1507 Å °0.016 Å °0.1907 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 185
2X-RAY DIFFRACTION1allA186
3X-RAY DIFFRACTION1allS1 - 139

+
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