[English] 日本語
Yorodumi
- PDB-9bnh: X-ray Crystal Structure of Cu-TZ4H tryptophan Zipper Metallo-Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bnh
TitleX-ray Crystal Structure of Cu-TZ4H tryptophan Zipper Metallo-Peptide
ComponentsCu-TZ4H tryptophan Zipper Metallo-Peptide
KeywordsDE NOVO PROTEIN / copper / beta-sheet / hairpin
Function / homologyACETIC ACID / COPPER (II) ION / AMMONIA / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsDang, V.T. / Nguyen, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Chemistry / Year: 2024
Title: Crystallography Reveals Metal-Triggered Restructuring of beta-Hairpins.
Authors: Thuc Dang, V. / Engineer, A. / McElheny, D. / Drena, A. / Telser, J. / Tomczak, K. / Nguyen, A.I.
History
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cu-TZ4H tryptophan Zipper Metallo-Peptide
B: Cu-TZ4H tryptophan Zipper Metallo-Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,18316
Polymers3,4062
Non-polymers77814
Water66737
1
A: Cu-TZ4H tryptophan Zipper Metallo-Peptide
hetero molecules

A: Cu-TZ4H tryptophan Zipper Metallo-Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,77912
Polymers3,4062
Non-polymers37310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area1830 Å2
ΔGint-29 kcal/mol
Surface area3210 Å2
MethodPISA
2
B: Cu-TZ4H tryptophan Zipper Metallo-Peptide
hetero molecules

B: Cu-TZ4H tryptophan Zipper Metallo-Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,58820
Polymers3,4062
Non-polymers1,18218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area2080 Å2
ΔGint-45 kcal/mol
Surface area3720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.198, 25.261, 24.149
Angle α, β, γ (deg.)90.000, 110.320, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-104-

NA

21B-109-

PGE

31A-205-

HOH

41B-208-

HOH

-
Components

-
Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Cu-TZ4H tryptophan Zipper Metallo-Peptide


Mass: 1702.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 51 molecules

#2: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH3
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Description: Cubic translucent crystals with light purple coloring
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystal Grown: 6.0 M Ammonium Nitrate, 0.1 M Sodium Acetate Trihydrate pH 4.6 (pH adjusted with HCl) Cryo-protection: 10% v/v PEG 400 (soaked)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2022
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→19.41 Å / Num. obs: 12507 / % possible obs: 97.98 % / Redundancy: 6.4 % / Biso Wilson estimate: 9.27 Å2 / CC1/2: 0.969 / CC star: 0.981 / Net I/σ(I): 19.7
Reflection shellResolution: 1.12→1.16 Å / Num. unique obs: 964 / CC1/2: 0.963 / CC star: 0.991 / % possible all: 94.32

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→16.48 Å / SU ML: 0.0731 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.3975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1447 1926 9.99 %
Rwork0.1195 17346 -
obs0.1222 19272 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.39 Å2
Refinement stepCycle: LAST / Resolution: 1.12→16.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms246 0 38 37 321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125318
X-RAY DIFFRACTIONf_angle_d0.8067425
X-RAY DIFFRACTIONf_chiral_restr0.072224
X-RAY DIFFRACTIONf_plane_restr0.004353
X-RAY DIFFRACTIONf_dihedral_angle_d6.351525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.150.18591290.16051170X-RAY DIFFRACTION91.61
1.15-1.180.1821390.14031216X-RAY DIFFRACTION97.9
1.18-1.210.1511460.14121313X-RAY DIFFRACTION98.92
1.21-1.250.20271300.1351211X-RAY DIFFRACTION98.82
1.25-1.30.15481500.1361276X-RAY DIFFRACTION99.1
1.3-1.350.14251320.12511259X-RAY DIFFRACTION99.14
1.35-1.410.14531410.12231238X-RAY DIFFRACTION98.64
1.41-1.490.14611380.10871281X-RAY DIFFRACTION99.23
1.49-1.580.12441460.11951189X-RAY DIFFRACTION95.09
1.58-1.70.13691330.11351245X-RAY DIFFRACTION96.57
1.7-1.870.13251310.1221241X-RAY DIFFRACTION98.21
1.87-2.140.11661390.11291255X-RAY DIFFRACTION98.59
2.14-2.690.14951330.11641244X-RAY DIFFRACTION96.63
2.7-16.480.15341390.11381208X-RAY DIFFRACTION94.99

+
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