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- PDB-9u78: Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with ... -

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Basic information

Entry
Database: PDB / ID: 9u78
TitleSingle Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
ComponentsSingle Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
KeywordsDE NOVO PROTEIN / Helix Bundles / Single Chain / Metalloprotein
Function / homologyACETATE ION / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDu, G.M. / Zhang, S.-Q. / Liu, L.J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177113 China
National Key R&D Program of China2024YFA0916800 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: A Designed Zn 2+ Sensor Domain Transmits Binding Information to Transmembrane Histidine Kinases.
Authors: Hatstat, A.K. / Kormos, R. / Xu, V. / Du, G. / Liu, L. / Zhang, S.Q. / DeGrado, W.F.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
B: Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,19011
Polymers28,6652
Non-polymers5259
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-9 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.748, 69.748, 55.048
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop


Mass: 14332.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Tascimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→49.06 Å / Num. obs: 39306 / % possible obs: 96.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.022 / Rrim(I) all: 0.048 / Χ2: 1.18 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 97.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.185 / Num. unique obs: 2098 / Rpim(I) all: 0.121 / Rrim(I) all: 0.206 / Χ2: 1.14 / Net I/σ(I) obs: 7.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1981 5.05 %
Rwork0.1765 --
obs0.1776 39233 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 28 198 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082126
X-RAY DIFFRACTIONf_angle_d0.9512878
X-RAY DIFFRACTIONf_dihedral_angle_d15.366847
X-RAY DIFFRACTIONf_chiral_restr0.059327
X-RAY DIFFRACTIONf_plane_restr0.009378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29621340.23932699X-RAY DIFFRACTION97
1.74-1.790.22591620.19412629X-RAY DIFFRACTION96
1.79-1.840.19781610.16662532X-RAY DIFFRACTION93
1.84-1.90.18881390.18042742X-RAY DIFFRACTION98
1.9-1.970.20691700.19362671X-RAY DIFFRACTION98
1.97-2.050.22341520.16682687X-RAY DIFFRACTION98
2.05-2.140.17161460.14622674X-RAY DIFFRACTION97
2.14-2.250.16331310.15782623X-RAY DIFFRACTION95
2.25-2.40.2061240.16942683X-RAY DIFFRACTION94
2.4-2.580.18911250.1692670X-RAY DIFFRACTION97
2.58-2.840.19411390.18162669X-RAY DIFFRACTION96
2.84-3.250.23351380.18672663X-RAY DIFFRACTION95
3.25-4.10.18261150.172666X-RAY DIFFRACTION95
4.1-49.060.19311450.18642644X-RAY DIFFRACTION93

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