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- PDB-2hvf: Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (N... -

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Basic information

Entry
Database: PDB / ID: 2hvf
TitleCrystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA
Components50S ribosomal protein L9
KeywordsSTRUCTURAL PROTEIN / L9 / ribosomal protein / NTL9 / G34dA
Function / homology
Function and homology information


cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / 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
ACETIC ACID / IMIDAZOLE / Large ribosomal subunit protein bL9
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phase from wild type NTL9 / Resolution: 1.57 Å
AuthorsAnil, B. / Kim, E.Y. / Cho, J.H. / Schindelin, H. / Raleigh, D.P.
CitationJournal: To be Published
Title: Detecting and quantifying strain in protein folding
Authors: Anil, B. / Kim, E.Y. / Cho, J.H. / Schindelin, H. / Raleigh, D.P.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 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 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details

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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)6,23411
Polymers5,7021
Non-polymers53310
Water1,15364
1


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

A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,46922
Polymers11,4032
Non-polymers1,06520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3640 Å2
ΔGint-348 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.517, 53.517, 36.178
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-423-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 50S ribosomal protein L9 / BL17


Mass: 5701.719 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: G34(DAL) / Source method: obtained synthetically
Details: This sequence naturally occurs in Bacillus stearothermophilus(Geobacillus stearothermophilus) with gene name rplI. It was chemically synthesized by FMOC solid-phase peptide synthesis method.
References: UniProt: P02417

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Non-polymers , 5 types, 74 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. all: 7705 / Num. obs: 7705 / % possible obs: 99.2 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.062 / Χ2: 1.23 / Net I/σ(I): 15.5
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.286 / Num. unique all: 684 / Χ2: 0.787 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: Phase from wild type NTL9 / Resolution: 1.57→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.776 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 355 4.6 %RANDOM
Rwork0.159 ---
all0.162 7670 --
obs0.162 7670 99.93 %-
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: 14.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 17 64 481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022422
X-RAY DIFFRACTIONr_bond_other_d0.0010.02402
X-RAY DIFFRACTIONr_angle_refined_deg1.6222561
X-RAY DIFFRACTIONr_angle_other_deg2.8713950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.449552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.88727.64717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8281589
X-RAY DIFFRACTIONr_chiral_restr0.0920.263
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0275
X-RAY DIFFRACTIONr_nbd_refined0.2690.286
X-RAY DIFFRACTIONr_nbd_other0.1730.2367
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2200
X-RAY DIFFRACTIONr_nbtor_other0.1020.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3870.237
X-RAY DIFFRACTIONr_metal_ion_refined0.1910.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.218
X-RAY DIFFRACTIONr_mcbond_it1.9741.5335
X-RAY DIFFRACTIONr_mcbond_other0.5681.5110
X-RAY DIFFRACTIONr_mcangle_it2.2262415
X-RAY DIFFRACTIONr_scbond_it3.6393185
X-RAY DIFFRACTIONr_scangle_it4.4614.5146
X-RAY DIFFRACTIONr_rigid_bond_restr1.7323962
X-RAY DIFFRACTIONr_sphericity_free8.58376
X-RAY DIFFRACTIONr_sphericity_bonded2.4543820
LS refinement shellResolution: 1.57→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 27 -
Rwork0.124 514 -
obs-541 100 %

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