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- PDB-7v4y: TTHA1264/TTHA1265 complex -

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Basic information

Entry
Database: PDB / ID: 7v4y
TitleTTHA1264/TTHA1265 complex
Components
  • Putative zinc protease
  • Zinc-dependent peptidase
KeywordsHYDROLASE / complex / close conformation
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / : / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc-dependent peptidase / Zinc protease
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, M. / Xu, Q. / Ran, T. / Wang, W. / Sun, B. / Wang, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770074 China
National Science Foundation (NSF, China)31770050 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal structures of TTHA1265 and TTHA1264/TTHA1265 complex reveal an intrinsic heterodimeric assembly.
Authors: Xu, M. / Xu, Q. / Wang, M. / Qiu, S. / Xu, D. / Zhang, W. / Wang, W. / He, J. / Wang, Q. / Ran, T. / Sun, B.
History
DepositionAug 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Zinc-dependent peptidase
A: Putative zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9003
Polymers93,8352
Non-polymers651
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-52 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.163, 87.163, 244.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Zinc-dependent peptidase


Mass: 46134.613 Da / Num. of mol.: 1 / Mutation: G32V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA1265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIU9
#2: Protein Putative zinc protease


Mass: 47700.043 Da / Num. of mol.: 1 / Mutation: E124G, F135L, S284T, D303V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA1264 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIV0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→19.98 Å / Num. obs: 37793 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.047 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5404 / CC1/2: 0.7 / Rpim(I) all: 0.47 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXv1.6refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HXK, 3EOQ

5hxk

3eoq


Resolution: 2.4→19.98 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.267 --
Rwork0.2308 --
obs-37750 99.41 %
Displacement parametersBiso mean: 52.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 1 178 6378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00986336
X-RAY DIFFRACTIONf_angle_d1.30128583
X-RAY DIFFRACTIONf_chiral_restr0.0788942
X-RAY DIFFRACTIONf_plane_restr0.00641136
X-RAY DIFFRACTIONf_dihedral_angle_d22.74933812

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