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- PDB-6j6a: Crystal structure of TldE from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 6j6a
TitleCrystal structure of TldE from Thermococcus kodakarensis
ComponentsZinc-dependent protease, TldD/PmbA family
KeywordsMETAL BINDING PROTEIN / metalloprotease
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / cytosol
Similarity search - Function
Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase C-terminal domain / PmbA/TldA metallopeptidase central domain
Similarity search - Domain/homology
Zinc-dependent protease, TldD/PmbA family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.353 Å
AuthorsZhang, X. / Liu, J.
CitationJournal: To Be Published
Title: Crystal structure of TldE from Thermococcus kodakarensis
Authors: Zhang, X. / Liu, J.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc-dependent protease, TldD/PmbA family
B: Zinc-dependent protease, TldD/PmbA family


Theoretical massNumber of molelcules
Total (without water)97,5082
Polymers97,5082
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-6 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.497, 104.497, 253.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Zinc-dependent protease, TldD/PmbA family


Mass: 48754.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0499 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02M Calcium Chloride, 0.1M Sodium Acetate pH 4.6, 30% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.353→31.931 Å / Num. obs: 59216 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.996 / Rpim(I) all: 0.052 / Net I/σ(I): 29.67
Reflection shellResolution: 2.353→2.437 Å / Num. unique obs: 2896 / CC1/2: 0.713 / Rpim(I) all: 0.508

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Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL4

1vl4


Resolution: 2.353→31.931 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.66
RfactorNum. reflection% reflection
Rfree0.2281 2000 3.38 %
Rwork0.1955 --
obs0.1966 59118 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.353→31.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 256 7110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086990
X-RAY DIFFRACTIONf_angle_d1.0149456
X-RAY DIFFRACTIONf_dihedral_angle_d4.3364212
X-RAY DIFFRACTIONf_chiral_restr0.0661042
X-RAY DIFFRACTIONf_plane_restr0.0071240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3526-2.41140.28841360.26693884X-RAY DIFFRACTION97
2.4114-2.47660.2971400.28034018X-RAY DIFFRACTION100
2.4766-2.54940.28141420.25464035X-RAY DIFFRACTION100
2.5494-2.63170.27911410.23814020X-RAY DIFFRACTION100
2.6317-2.72570.28441410.22844017X-RAY DIFFRACTION100
2.7257-2.83480.28031410.22964064X-RAY DIFFRACTION100
2.8348-2.96370.26641420.21844021X-RAY DIFFRACTION100
2.9637-3.11980.2621420.21544070X-RAY DIFFRACTION100
3.1198-3.31510.22861430.20314061X-RAY DIFFRACTION100
3.3151-3.57080.22641420.18584092X-RAY DIFFRACTION100
3.5708-3.92950.2171450.17394112X-RAY DIFFRACTION100
3.9295-4.49680.21141440.16874131X-RAY DIFFRACTION100
4.4968-5.66030.1991470.17684195X-RAY DIFFRACTION100
5.6603-31.93420.18111540.1754398X-RAY DIFFRACTION100

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