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- PDB-7cay: Crystal Structure of Lon N-terminal domain protein from Xanthomon... -

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Basic information

Entry
Database: PDB / ID: 7cay
TitleCrystal Structure of Lon N-terminal domain protein from Xanthomonas campestris
ComponentsATP-dependent protease
KeywordsPROTEIN BINDING / N-terminal domain / Lon protease
Function / homologyLon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / peptidase activity / ATP-dependent protease / Lon N-terminal domain-containing protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSingh, R. / Sharma, B. / Deshmukh, S. / Kumar, A. / Makde, R.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase.
Authors: Singh, R. / Deshmukh, S. / Kumar, A. / Goyal, V.D. / Makde, R.D.
History
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: ATP-dependent protease


Theoretical massNumber of molelcules
Total (without water)21,3181
Polymers21,3181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration and PISA analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.925, 124.925, 55.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein ATP-dependent protease


Mass: 21318.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: D0A42_17175 / Plasmid: pST50Tr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A3E1KP83, UniProt: Q8P5P7*PLUS

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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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8.5
Details: Isopropanol 35%, 200mM ammonium acetate, 100 mM Tris-Cl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 7, 2016 / Details: mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→44.17 Å / Num. obs: 5595 / % possible obs: 99 % / Redundancy: 8.2 % / Biso Wilson estimate: 74.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Net I/σ(I): 19.9 / Num. measured all: 46030 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.958.40.90567117950.8590.3250.9632.399.6
8.85-44.177.10.02614262010.9990.010.02857.195.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zbo

1zbo


Resolution: 2.8→33.327 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 320 5.73 %
Rwork0.2618 5268 -
obs0.2634 5588 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 71.1476 Å2 / Biso min: 48.99 Å2
Refinement stepCycle: final / Resolution: 2.8→33.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 0 0 1262
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021285
X-RAY DIFFRACTIONf_angle_d0.5691751
X-RAY DIFFRACTIONf_chiral_restr0.038207
X-RAY DIFFRACTIONf_plane_restr0.003226
X-RAY DIFFRACTIONf_dihedral_angle_d16.076759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Num. reflection Rfree: 160

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-3.52720.34950.327257699
3.5272-33.30.27090.2417269298
Refinement TLS params.Method: refined / Origin x: -30.9683 Å / Origin y: 11.2254 Å / Origin z: -6.3041 Å
111213212223313233
T0.3464 Å20.1149 Å2-0.086 Å2-0.473 Å2-0.0766 Å2--0.42 Å2
L2.6554 °2-0.1753 °2-1.4969 °2-2.1053 °2-0.5906 °2--3.8025 °2
S0.0347 Å °0.008 Å °0.1722 Å °0.0207 Å °-0.0103 Å °0.3566 Å °-0.3183 Å °-0.6616 Å °-0.0157 Å °
Refinement TLS groupSelection details: all

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