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- PDB-36iw: Crystal structure of a large ribosomal subunit protein bL17 from ... -

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Basic information

Entry
Database: PDB / ID: 36iw
TitleCrystal structure of a large ribosomal subunit protein bL17 from Bordetella pertussis
ComponentsLarge ribosomal subunit protein bL17
KeywordsRIBOSOMAL PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / large ribosomal subunit protein bL17 / Bordetella pertussis
Function / homology: / Ribosomal protein L17 signature. / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / Large ribosomal subunit protein bL17
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Crystal structure of a large ribosomal subunit protein bL17 from Bordetella pertussis
Authors: Lanyi Lari, N. / Ung, A.R. / Lovell, S. / Battaile, K.P.
History
DepositionJun 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large ribosomal subunit protein bL17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8654
Polymers14,7581
Non-polymers1063
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.194, 73.010, 52.486
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-313-

HOH

21A-357-

HOH

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Components

#1: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14758.317 Da / Num. of mol.: 1 / Fragment: M1-E120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: rplQ, BP3643 / Plasmid: BopeA.17872.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7VTA6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.73 Å3/Da / Density % sol: 28.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3M NaCl, 100mM Bis-Tris pH 5.5, BopeA.17872.a.B2.PW39472 at 11.5 mg/mL. Plate 20708 G12 drop 1, Puck: PSL-0509, Cryo: 20% glycerol + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 30, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→42.99 Å / Num. obs: 12571 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Χ2: 1.01 / Net I/σ(I): 20 / Num. measured all: 165508
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 96.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 1.453 / Num. measured all: 7074 / Num. unique obs: 595 / CC1/2: 0.672 / Rpim(I) all: 0.435 / Rrim(I) all: 1.519 / Χ2: 0.98 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(dev_6082: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→42.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 637 5.07 %
Rwork0.1868 --
obs0.1883 12557 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 3 57 912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008869
X-RAY DIFFRACTIONf_angle_d0.9151168
X-RAY DIFFRACTIONf_dihedral_angle_d8.209123
X-RAY DIFFRACTIONf_chiral_restr0.053132
X-RAY DIFFRACTIONf_plane_restr0.013151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.780.34961240.2832315X-RAY DIFFRACTION98
1.78-1.960.261400.22222333X-RAY DIFFRACTION99
1.96-2.240.23221400.18952347X-RAY DIFFRACTION100
2.24-2.820.20881270.19442410X-RAY DIFFRACTION100
2.82-42.990.20451060.17262515X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.4724-4.70640.38553.2961-0.58292.3027-0.12850.1783-0.3684-0.1361-0.1311-0.43110.38930.79590.22010.33780.03810.03190.33850.03790.296820.29226.8185-9.3754
24.11480.9352-3.74262.4117-1.60463.7358-0.31890.2199-0.4248-0.1628-0.1155-0.21510.3723-0.11880.50430.27140.0080.01530.2847-0.03360.277611.8916.0592-12.335
39.0684-0.8822-4.06672.1902-2.12778.5252-0.1477-0.3387-0.0460.4225-0.0858-0.3247-0.03250.33010.1510.2495-0.031-0.05420.1877-0.00050.248613.70628.44793.3502
45.8603-0.7645-1.83233.41460.91595.5019-0.0850.51310.0324-0.42040.0599-0.34440.29430.1454-0.02120.22490.02510.02530.1655-0.00960.201610.070811.6935-16.6138
53.68414.61722.02777.477-0.75097.519-0.1008-0.85062.116-0.15191.1082-1.1372-2.18371.4353-0.85850.9217-0.08620.11840.4824-0.280.89999.033520.6289-12.0489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 120 )

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