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- PDB-2q7f: Crystal structure of YrrB: a TPR protein with an unusual peptide-... -

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Basic information

Entry
Database: PDB / ID: 2q7f
TitleCrystal structure of YrrB: a TPR protein with an unusual peptide-binding site
ComponentsYrrB protein
KeywordsPROTEIN BINDING / TPR / YRRB
Function / homology
Function and homology information


: / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
TPR repeat-containing protein YrrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsOh, J. / Han, D. / Kim, K. / Lim, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of YrrB: A TPR protein with an unusual peptide-binding site
Authors: Han, D. / Oh, J. / Kim, K. / Lim, H. / Kim, Y.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YrrB protein
B: YrrB protein


Theoretical massNumber of molelcules
Total (without water)54,2852
Polymers54,2852
Non-polymers00
Water1,00956
1
A: YrrB protein


Theoretical massNumber of molelcules
Total (without water)27,1431
Polymers27,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YrrB protein


Theoretical massNumber of molelcules
Total (without water)27,1431
Polymers27,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.938, 85.139, 69.048
Angle α, β, γ (deg.)90.00, 130.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 43 - 236 / Label seq-ID: 42 - 235

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein YrrB protein


Mass: 27142.504 Da / Num. of mol.: 2 / Fragment: sequence database residues 4-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yrrB / Plasmid: PET 28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON PLUS RIL / References: UniProt: O34452
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.8
Details: 40MM PHOTASSIUM PHOSPHATE(KH2PO4), 4% PEG 6000, 20% GLYCEROL, PH 4.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 4.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 14817 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1183 / % possible all: 76.7

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.49→28.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.117 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.004 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1488 10 %RANDOM
Rwork0.206 ---
obs0.211 13328 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.05 Å2
2---0.52 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.49→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 0 56 3104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8445386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26825.769156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99115544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.481510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22170
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4351.51977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80223056
X-RAY DIFFRACTIONr_scbond_it1.04331264
X-RAY DIFFRACTIONr_scangle_it1.7764.51134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
776medium positional0.360.5
749loose positional0.75
776medium thermal0.672
749loose thermal1.2310
LS refinement shellResolution: 2.49→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 90 -
Rwork0.275 749 -
obs--73.34 %
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)
11.0985-0.36020.0813.55090.06040.1411-0.06130.2691-0.3028-0.08520.05860.08240.08270.1170.00270.00510.0316-0.01270.0478-0.0293-0.02517.196752.530315.6273
20.9785-0.1655-0.1742.1922-1.42791.8062-0.0366-0.08990.1993-0.01580.00440.01610.02080.08520.0322-0.08690.0354-0.0244-0.0323-0.0095-0.133513.983274.094640.2465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA44 - 6143 - 60
2X-RAY DIFFRACTION1AA62 - 23661 - 235
3X-RAY DIFFRACTION2BB44 - 6143 - 60
4X-RAY DIFFRACTION2BB62 - 23661 - 235

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