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- PDB-2hbb: Crystal Structure of the N-terminal Domain of Ribosomal Protein L... -

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Basic information

Entry
Database: PDB / ID: 2hbb
TitleCrystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9)
Components50S ribosomal protein L9
KeywordsRNA BINDING PROTEIN / L9 / ribosomal protein / NTL9
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Ribosomal protein L9, N-terminal domain / Ribosomal Protein L9; domain 1 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal ...Ribosomal protein L9, N-terminal domain / Ribosomal Protein L9; domain 1 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL9
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, J.-H. / Kim, E.Y. / Schindelin, H. / Raleigh, D.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Energetically significant networks of coupled interactions within an unfolded protein.
Authors: Cho, J.H. / Meng, W. / Sato, S. / Kim, E.Y. / Schindelin, H. / Raleigh, D.P.
#1: Journal: Biochemistry / Year: 2009
Title: Interpretation of p-cyanophenylalanine fluorescence in proteins in terms of solvent exposure and contribution of side-chain quenchers: a combined fluorescence, IR and molecular dynamics study.
Authors: Taskent-Sezgin, H. / Chung, J. / Patsalo, V. / Miyake-Stoner, S.J. / Miller, A.M. / Brewer, S.H. / Mehl, R.A. / Green, D.F. / Raleigh, D.P. / Carrico, I.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Aug 13, 2014Group: Database references
Revision 1.5Sep 24, 2014Group: Database references
Revision 1.6Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.7Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8215
Polymers5,5601
Non-polymers2624
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,64210
Polymers11,1192
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1910 Å2
ΔGint-195 kcal/mol
Surface area5930 Å2
MethodPISA, PQS
3
A: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,64210
Polymers11,1192
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area610 Å2
ΔGint-147 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.918, 53.918, 36.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-135-

HOH

21A-152-

HOH

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Components

#1: Protein 50S ribosomal protein L9 / / BL17


Mass: 5559.564 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: rplI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02417
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2006
Radiation
IDProtocolScattering typeWavelength-ID
1Single wavelenthx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 4752 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.079 / Χ2: 1.112 / Net I/σ(I): 16.4
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.345 / Num. unique all: 406 / Χ2: 1.066 / % possible all: 85.8

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Phasing

Phasing MRRfactor: 0.586 / Cor.coef. Fo:Fc: 0.267
Highest resolutionLowest resolution
Rotation3.5 Å38.13 Å
Translation3.5 Å38.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.56 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 202 4.5 %RANDOM
Rwork0.197 ---
all0.199 ---
obs0.199 4526 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms390 0 4 52 446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022394
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.989523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.636550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.27527.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2581583
X-RAY DIFFRACTIONr_chiral_restr0.0960.258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02277
X-RAY DIFFRACTIONr_nbd_refined0.2210.2153
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3940.228
X-RAY DIFFRACTIONr_metal_ion_refined0.060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0810.21
X-RAY DIFFRACTIONr_mcbond_it1.1511.5255
X-RAY DIFFRACTIONr_mcangle_it1.9152393
X-RAY DIFFRACTIONr_scbond_it3.293150
X-RAY DIFFRACTIONr_scangle_it5.7974.5130
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 11 -
Rwork0.217 307 -
obs-318 99.07 %

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