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- PDB-6nqc: Crystal structure of a peptidase from an acI-B1 Actinobacterium -

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Basic information

Entry
Database: PDB / ID: 6nqc
TitleCrystal structure of a peptidase from an acI-B1 Actinobacterium
ComponentsCyanophycinase-like exopeptidase
KeywordsHYDROLASE / Peptidase
Function / homologyPeptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like / serine-type peptidase activity / Cysnophycinase-like exopeptidase
Function and homology information
Biological speciesactinobacterium SCGC AAA027-L06 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsForest, K.T. / Dwulit-Smith, J.R. / Satyshur, K.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1518160 United States
CitationJournal: To Be Published
Title: Structure of a peptidase from an acI-B1 Actinobacterium
Authors: Dwulit-Smith, J. / Satyshur, K.A. / McMahon, K.D. / Forest, K.T.
History
DepositionJan 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanophycinase-like exopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7412
Polymers28,6451
Non-polymers961
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.693, 88.916, 131.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein Cyanophycinase-like exopeptidase


Mass: 28645.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) actinobacterium SCGC AAA027-L06 (bacteria)
Gene: A27L6_002500000020 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9H630
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.28 Å3/Da / Density % sol: 46.04 % / Description: Long rods growing in clusters.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals of enzyme grew after mixing 2 microliters 16 mg/ml protein in buffer (30 mM maleic acid [pH 6.7], 200 mM Na2SO4) with an equal volume of condition 7 (100 mM HEPES-NaOH [pH 7.5], 2% ...Details: Crystals of enzyme grew after mixing 2 microliters 16 mg/ml protein in buffer (30 mM maleic acid [pH 6.7], 200 mM Na2SO4) with an equal volume of condition 7 (100 mM HEPES-NaOH [pH 7.5], 2% v/v PEG 400, 2 M (NH4)2SO4) from the TOP96 screen (Anatrace) over 500 microliters of the screen solution. 0.5 microliters IZIT crystal dye (Hampton) was added to the crystal-containing droplet after 4 weeks

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.94→26.5 Å / Num. obs: 18380 / % possible obs: 91.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 26.4
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.14 / Num. unique obs: 953 / CC1/2: 0.915 / Rpim(I) all: 0.303 / Rrim(I) all: 0.805 / Χ2: 0.793 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIX(1.14_3260: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3l4e

3l4e


Resolution: 1.94→26.409 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2265 917 5.01 %
Rwork0.1638 --
obs0.1668 18310 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.94→26.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 5 163 2060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111948
X-RAY DIFFRACTIONf_angle_d1.0232644
X-RAY DIFFRACTIONf_dihedral_angle_d5.3591590
X-RAY DIFFRACTIONf_chiral_restr0.061288
X-RAY DIFFRACTIONf_plane_restr0.007345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.03260.22351340.17852554X-RAY DIFFRACTION95
2.0326-2.15990.20891390.16512638X-RAY DIFFRACTION99
2.1599-2.32660.3063950.21161771X-RAY DIFFRACTION66
2.3266-2.56050.23571390.15952656X-RAY DIFFRACTION98
2.5605-2.93060.19711420.1642698X-RAY DIFFRACTION99
2.9306-3.69070.27141330.16852522X-RAY DIFFRACTION93
3.6907-26.4110.19551350.14762554X-RAY DIFFRACTION93

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