[English] 日本語
Yorodumi
- PDB-9db9: Ni-Bound Structure of Computationally Designed Homotrimer Tet4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9db9
TitleNi-Bound Structure of Computationally Designed Homotrimer Tet4
ComponentsComputationally Designed Tet4
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsHoffnagle, A.M. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: Biochemistry / Year: 2025
Title: A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity.
Authors: Hoffnagle, A.M. / Srisantitham, S. / Neeley, M. / Tsai, C.Y. / Tezcan, F.A.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Computationally Designed Tet4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6202
Polymers12,5621
Non-polymers591
Water1267
1
A: Computationally Designed Tet4
hetero molecules

A: Computationally Designed Tet4
hetero molecules

A: Computationally Designed Tet4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8616
Polymers37,6853
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3940 Å2
ΔGint-58 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.930, 71.930, 55.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-302-

HOH

-
Components

#1: Protein Computationally Designed Tet4


Mass: 12561.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 400, 200 mM NaCl, 100 mM Bis-Tris (pH 5.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.48515 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48515 Å / Relative weight: 1
ReflectionResolution: 2.41→41.55 Å / Num. obs: 8250 / % possible obs: 99.98 % / Redundancy: 9.9 % / Biso Wilson estimate: 74.77 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06804 / Rpim(I) all: 0.02266 / Rrim(I) all: 0.07177 / Net I/σ(I): 18.19
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.9265 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1292 / CC1/2: 0.758 / CC star: 0.929 / Rpim(I) all: 0.3083 / Rrim(I) all: 0.9773 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→41.55 Å / SU ML: 0.4033 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 34.508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 819 9.93 %
Rwork0.2247 7428 -
obs0.2294 8247 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.18 Å2
Refinement stepCycle: LAST / Resolution: 2.41→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 1 7 826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018847
X-RAY DIFFRACTIONf_angle_d0.47811148
X-RAY DIFFRACTIONf_chiral_restr0.0308134
X-RAY DIFFRACTIONf_plane_restr0.0027143
X-RAY DIFFRACTIONf_dihedral_angle_d18.8189315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.560.3711340.35571220X-RAY DIFFRACTION100
2.57-2.760.40571340.34391258X-RAY DIFFRACTION100
2.77-3.040.42241360.33571232X-RAY DIFFRACTION100
3.04-3.480.33741340.29981244X-RAY DIFFRACTION100
3.48-4.370.30841400.21341210X-RAY DIFFRACTION100
4.39-41.550.18081410.171264X-RAY DIFFRACTION99.65
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)
16.38783099324.75025819333.585569244278.3034530538-1.177884237145.07180507715-0.5657505294321.427466879610.333041633549-0.0143429278560.8028677354040.859560335652-0.712936242376-0.470387528427-0.1468131534940.594156981322-0.087258428482-0.1079449155230.8424582807220.09760916971970.653402103021-7.02133883018-7.79045729909-6.55097167874
28.970920973811.892505385631.408837699277.8814821092-0.5241378458955.99623577366-0.191273092504-0.586729612305-0.5904765434211.290371134040.3213755418671.57445213132-0.0293819065842-0.65471756703-0.08465437292340.9660172575720.1521953842360.1253963305190.470039732369-0.05523624864141.04401214538-7.44280809677-13.65918692515.43548180791
35.621611493684.999257432734.303969818847.353585512820.9757052816026.174251450920.4173918561341.7457398215-0.4469675358490.570924367480.8706887422350.005990296691841.93991407836-0.730182078331-0.9324829687820.864904381055-0.0783124247071-0.05073184670240.887672160555-0.09082716032810.822510785159-6.55830243391-17.495487064-7.05666779197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 107 )

+
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