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- PDB-5hxk: Structure of TTHA1265 -

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Basic information

Entry
Database: PDB / ID: 5hxk
TitleStructure of TTHA1265
ComponentsZinc-dependent peptidase
KeywordsHYDROLASE / TTHA1265 / protease / complex
Function / homology: / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / metal ion binding / Zinc-dependent peptidase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWang, W.W. / Ran, T.T. / Xu, D.Q. / Wang, M.T.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170686 China
National Natural Science Foundation of China31400055 China
National Natural Science Foundation of China31100028 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
CitationJournal: To Be Published
Title: Structure of TTHA1264-1265 complex
Authors: Ran, T.T. / Wang, W.W. / Xu, D.Q. / Wang, M.T.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc-dependent peptidase
B: Zinc-dependent peptidase
C: Zinc-dependent peptidase


Theoretical massNumber of molelcules
Total (without water)138,2783
Polymers138,2783
Non-polymers00
Water12,791710
1
A: Zinc-dependent peptidase

A: Zinc-dependent peptidase


Theoretical massNumber of molelcules
Total (without water)92,1852
Polymers92,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area5260 Å2
ΔGint-22 kcal/mol
Surface area32210 Å2
MethodPISA
2
B: Zinc-dependent peptidase
C: Zinc-dependent peptidase


Theoretical massNumber of molelcules
Total (without water)92,1852
Polymers92,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-27 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.544, 116.544, 165.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

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Components

#1: Protein Zinc-dependent peptidase


Mass: 46092.535 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1265 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIU9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.65 % / Description: rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 10000, Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 88245 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.661 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.225 4285 4.86 %
Rwork0.187 --
obs0.1889 88190 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9279 0 0 710 9989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089486
X-RAY DIFFRACTIONf_angle_d0.93212849
X-RAY DIFFRACTIONf_dihedral_angle_d16.9285775
X-RAY DIFFRACTIONf_chiral_restr0.051419
X-RAY DIFFRACTIONf_plane_restr0.0061698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.28061350.27352749X-RAY DIFFRACTION100
2.0227-2.04650.3131500.26792795X-RAY DIFFRACTION100
2.0465-2.07140.28681420.25222754X-RAY DIFFRACTION100
2.0714-2.09760.30771280.2452750X-RAY DIFFRACTION100
2.0976-2.12520.23611320.22692797X-RAY DIFFRACTION100
2.1252-2.15420.25621330.22752769X-RAY DIFFRACTION100
2.1542-2.1850.27671330.22912770X-RAY DIFFRACTION100
2.185-2.21760.29211500.2252764X-RAY DIFFRACTION100
2.2176-2.25220.31211220.25492804X-RAY DIFFRACTION100
2.2522-2.2890.28361420.23512777X-RAY DIFFRACTION100
2.289-2.32840.27241470.21072775X-RAY DIFFRACTION100
2.3284-2.37070.25051620.20172745X-RAY DIFFRACTION100
2.3707-2.41620.25251360.1992776X-RAY DIFFRACTION100
2.4162-2.46550.24681660.19462779X-RAY DIFFRACTION100
2.4655-2.5190.24361640.19332720X-RAY DIFFRACTION100
2.519-2.57740.24781510.19112790X-RAY DIFFRACTION100
2.5774-2.64170.26821220.1982811X-RAY DIFFRACTION100
2.6417-2.7130.24741490.18682782X-RAY DIFFRACTION100
2.713-2.79260.24711150.19082796X-RAY DIFFRACTION100
2.7926-2.88250.27221380.19362811X-RAY DIFFRACTION100
2.8825-2.98520.22891510.19082801X-RAY DIFFRACTION100
2.9852-3.10420.19821470.18412771X-RAY DIFFRACTION100
3.1042-3.24490.22631400.18442808X-RAY DIFFRACTION100
3.2449-3.41520.2381250.18092831X-RAY DIFFRACTION100
3.4152-3.62790.19331340.16892843X-RAY DIFFRACTION100
3.6279-3.9060.17581510.15932814X-RAY DIFFRACTION100
3.906-4.29540.17721460.14942833X-RAY DIFFRACTION100
4.2954-4.90840.18121700.14732825X-RAY DIFFRACTION100
4.9084-6.15250.20741490.16982892X-RAY DIFFRACTION100
6.1525-100.17141550.15712973X-RAY DIFFRACTION100

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