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- PDB-5inx: A C69-family cysteine dipeptidase in complex with Met and Ala fro... -

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Basic information

Entry
Database: PDB / ID: 5inx
TitleA C69-family cysteine dipeptidase in complex with Met and Ala from Lactobacillus farciminis
ComponentsDipeptidase
KeywordsHYDROLASE / C69 family / cysteine dipeptidase / Ntn hydrolase / Lactobacillus farciminis / Gly-Pro
Function / homologyALANINE / METHIONINE / :
Function and homology information
Biological speciesLactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.681 Å
AuthorsKono, R. / Watanabe, K.
CitationJournal: To Be Published
Title: A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation
Authors: Kono, R. / Watanabe, K.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidase
B: Dipeptidase
C: Dipeptidase
D: Dipeptidase
E: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,71315
Polymers264,5225
Non-polymers1,19210
Water53,3242960
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-54 kcal/mol
Surface area86340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.650, 182.415, 98.215
Angle α, β, γ (deg.)90.00, 112.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1036-

HOH

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Components

#1: Protein
Dipeptidase


Mass: 52904.344 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria)
Strain: KCTC 3681 = DSM 20184 / Gene: FC68_GL001211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R1IQH8
#2: Chemical
ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H11NO2S / Details: Substrate
#3: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO2 / Details: Substrate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2960 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.8 M 1,6-hexanediol, 10 mM CoCl2, 100 mM acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→39.314 Å / Num. obs: 368718 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.29
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IAU

5iau


Resolution: 1.681→39.314 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1805 15099 4.95 %
Rwork0.1584 --
obs0.1595 304777 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.681→39.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18355 0 0 2960 21315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718759
X-RAY DIFFRACTIONf_angle_d1.06525530
X-RAY DIFFRACTIONf_dihedral_angle_d11.7556825
X-RAY DIFFRACTIONf_chiral_restr0.0462800
X-RAY DIFFRACTIONf_plane_restr0.0053400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6807-1.69980.2324770.19019296X-RAY DIFFRACTION95
1.6998-1.71980.22935260.18739663X-RAY DIFFRACTION99
1.7198-1.74080.2064960.17499589X-RAY DIFFRACTION99
1.7408-1.76280.20724910.17369583X-RAY DIFFRACTION99
1.7628-1.7860.20095040.17189668X-RAY DIFFRACTION99
1.786-1.81050.20924950.17819629X-RAY DIFFRACTION99
1.8105-1.83640.18935030.17039621X-RAY DIFFRACTION99
1.8364-1.86380.19924780.17129686X-RAY DIFFRACTION99
1.8638-1.89290.20215150.16679564X-RAY DIFFRACTION99
1.8929-1.92390.22135150.1729636X-RAY DIFFRACTION99
1.9239-1.95710.19175220.16319596X-RAY DIFFRACTION99
1.9571-1.99270.18985380.15939593X-RAY DIFFRACTION99
1.9927-2.0310.18265020.15689683X-RAY DIFFRACTION99
2.031-2.07250.20614920.15979613X-RAY DIFFRACTION99
2.0725-2.11750.19294970.15869584X-RAY DIFFRACTION99
2.1175-2.16680.17794630.15069728X-RAY DIFFRACTION99
2.1668-2.2210.18984800.15939624X-RAY DIFFRACTION99
2.221-2.2810.1775040.169680X-RAY DIFFRACTION99
2.281-2.34810.1765510.1549618X-RAY DIFFRACTION99
2.3481-2.42390.19345000.15389695X-RAY DIFFRACTION100
2.4239-2.51050.19055260.15829679X-RAY DIFFRACTION100
2.5105-2.6110.18574810.15719720X-RAY DIFFRACTION100
2.611-2.72980.18354880.16489815X-RAY DIFFRACTION100
2.7298-2.87370.17724850.15999711X-RAY DIFFRACTION100
2.8737-3.05370.19294640.16329766X-RAY DIFFRACTION100
3.0537-3.28940.17745140.15979734X-RAY DIFFRACTION100
3.2894-3.62020.15825150.15279750X-RAY DIFFRACTION100
3.6202-4.14350.15395330.14519747X-RAY DIFFRACTION100
4.1435-5.21850.14045330.13719738X-RAY DIFFRACTION100
5.2185-39.32450.18755110.16599669X-RAY DIFFRACTION98

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