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- PDB-6xhz: Alpha-lytic protease homolog N4 -

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Basic information

Entry
Database: PDB / ID: 6xhz
TitleAlpha-lytic protease homolog N4
ComponentsN4: hypothetical protein
KeywordsUNKNOWN FUNCTION / Pseudoprotease / trypsin-like fold
Biological speciesStreptomyces monomycini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNixon, C.F. / Marqusee, S.M. / Gee, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM050945 United States
CitationJournal: Biochemistry / Year: 2021
Title: Exploring the Evolutionary History of Kinetic Stability in the alpha-Lytic Protease Family.
Authors: Nixon, C.F. / Lim, S.A. / Sailer, Z.R. / Zheludev, I.N. / Gee, C.L. / Kelch, B.A. / Harms, M.J. / Marqusee, S.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N4: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9262
Polymers21,8301
Non-polymers961
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.121, 41.695, 51.175
Angle α, β, γ (deg.)90.000, 98.618, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein N4: hypothetical protein


Mass: 21830.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces monomycini (bacteria) / Gene: hypothetical protein [Streptomyces monomycini]. / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)pLysS
#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.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2019
RadiationMonochromator: S111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→41.7 Å / Num. obs: 39417 / % possible obs: 86.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.303 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 14.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 625 / CC1/2: 0.278 / Rpim(I) all: 1.034 / Rrim(I) all: 1.462 / % possible all: 27.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGB

3sgb


Resolution: 1.25→38.68 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1873 1934 4.91 %
Rwork0.1704 37449 -
obs0.1713 39383 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.93 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 5 184 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861405
X-RAY DIFFRACTIONf_angle_d0.95561922
X-RAY DIFFRACTIONf_chiral_restr0.0794220
X-RAY DIFFRACTIONf_plane_restr0.0065255
X-RAY DIFFRACTIONf_dihedral_angle_d17.0942494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.3721600.4445905X-RAY DIFFRACTION30.01
1.28-1.310.366860.32711529X-RAY DIFFRACTION50.05
1.31-1.350.29481050.29392008X-RAY DIFFRACTION64.9
1.35-1.40.26641170.25312400X-RAY DIFFRACTION78.26
1.4-1.450.27761370.22872955X-RAY DIFFRACTION96.17
1.45-1.50.22691670.20983099X-RAY DIFFRACTION99.97
1.5-1.570.20551380.19333060X-RAY DIFFRACTION99.88
1.57-1.650.20391680.18483080X-RAY DIFFRACTION99.78
1.65-1.760.2041650.18073048X-RAY DIFFRACTION99.54
1.76-1.890.18661430.16583091X-RAY DIFFRACTION99.02
1.89-2.080.16491700.15623053X-RAY DIFFRACTION98.96
2.08-2.390.17381740.15333043X-RAY DIFFRACTION98.8
2.39-3.010.17051460.16223099X-RAY DIFFRACTION98.24
3.01-38.680.16941580.15073079X-RAY DIFFRACTION97.29

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