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

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Basic information

Entry
Database: PDB / ID: 2hba
TitleCrystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M
Components50S ribosomal protein L9
KeywordsRNA BINDING PROTEIN / L9 / ribosomal protein / NTL9 / K12M
Function / homology
Function and homology information


rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
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 / Ribosomal protein L9, N-terminal domain superfamily / 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 / Ribosomal protein L9, N-terminal domain superfamily / 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
IMIDAZOLE / Large ribosomal subunit protein bL9
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.25 Å
AuthorsCho, J.-H. / Kim, E.Y. / Schindelin, H. / Raleigh, D.P.
CitationJournal: 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.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4Sep 24, 2014Group: Database references
Revision 1.5Oct 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 1.6Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_asym_id / _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_asym_id / _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_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L9
B: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,32621
Polymers11,3792
Non-polymers94719
Water1,71195
1
A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0288
Polymers5,6901
Non-polymers3387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,29913
Polymers5,6901
Non-polymers60912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: 50S ribosomal protein L9
hetero molecules

B: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65342
Polymers22,7594
Non-polymers1,89438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation7_454-x-1/2,y+1/2,-z-1/21
Buried area7950 Å2
ΔGint-666 kcal/mol
Surface area11220 Å2
MethodPISA
4
B: 50S ribosomal protein L9
hetero molecules

B: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules

A: 50S ribosomal protein L9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65342
Polymers22,7594
Non-polymers1,89438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area5040 Å2
ΔGint-686 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.614, 74.416, 50.755
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-227-

HOH

21B-307-

HOH

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Components

#1: Protein 50S ribosomal protein L9 / BL17


Mass: 5689.709 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: K12M
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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 8.1 % / Av σ(I) over netI: 11.4 / Number: 107776 / Rmerge(I) obs: 0.079 / Χ2: 0.85 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 8443 / % possible obs: 97.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.245010010.0311.2357.7
4.956.2410010.0470.6569.4
4.334.9510010.0490.6919.6
3.934.3310010.0470.6399.9
3.653.9310010.060.7989.9
3.443.6510010.0690.7810.1
3.263.4410010.0840.8229
3.123.2610010.0980.8695.7
33.1210010.1120.8864.1
2.9310010.1350.8853.1
2.812.910010.1650.895
2.732.8110010.1850.914
2.662.7399.510.2180.918
2.592.6699.610.1950.902
2.532.5999.810.2140.904
2.482.539810.220.939
2.432.4895.310.2160.818
2.382.4390.610.2440.886
2.342.3885.310.230.795
2.32.3476.210.2991.018
ReflectionResolution: 1.25→50 Å / Num. all: 26328 / Num. obs: 26328 / % possible obs: 94.6 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.056 / Χ2: 1.234 / Net I/σ(I): 23.6
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3 / Num. unique all: 1904 / Χ2: 0.887 / % possible all: 69.9

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.74 / FOM acentric: 0.75 / FOM centric: 0.71 / Reflection: 1372 / Reflection acentric: 1059 / Reflection centric: 313
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-19.8840.790.820.75593227
6.3-100.70.710.719813365
5-6.30.720.720.7322917356
4.4-50.770.780.7323518649
3.8-4.40.770.780.7240633175
3.5-3.80.70.710.6324520441

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: SIRAS / Resolution: 1.25→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.028 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1306 5 %RANDOM
Rwork0.144 ---
all0.145 ---
obs0.145 26264 94.7 %-
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: 15.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.95 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 23 95 914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022824
X-RAY DIFFRACTIONr_bond_other_d0.0010.02793
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9921090
X-RAY DIFFRACTIONr_angle_other_deg1.75531876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8425102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38427.57633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58915180
X-RAY DIFFRACTIONr_chiral_restr0.1410.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined0.280.2160
X-RAY DIFFRACTIONr_nbd_other0.1770.2695
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2395
X-RAY DIFFRACTIONr_nbtor_other0.0960.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3840.260
X-RAY DIFFRACTIONr_metal_ion_refined0.280.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7010.211
X-RAY DIFFRACTIONr_mcbond_it3.2263675
X-RAY DIFFRACTIONr_mcbond_other1.7143220
X-RAY DIFFRACTIONr_mcangle_it3.3374805
X-RAY DIFFRACTIONr_scbond_it4.5666362
X-RAY DIFFRACTIONr_scangle_it5.5968285
X-RAY DIFFRACTIONr_rigid_bond_restr3.18231905
X-RAY DIFFRACTIONr_sphericity_free11.313114
X-RAY DIFFRACTIONr_sphericity_bonded4.28331609
LS refinement shellResolution: 1.25→1.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 68 -
Rwork0.234 1253 -
obs-1321 66.12 %

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