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- PDB-1hus: RIBOSOMAL PROTEIN S7 -

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Basic information

Entry
Database: PDB / ID: 1hus
TitleRIBOSOMAL PROTEIN S7
ComponentsRIBOSOMAL PROTEIN S7
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING PROTEIN / DECODING CENTER
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD WITH SE-MET MUTANT / Resolution: 2.5 Å
AuthorsHosaka, H. / Nakagawa, A. / Tanaka, I.
Citation
Journal: Structure / Year: 1997
Title: Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor.
Authors: Hosaka, H. / Nakagawa, A. / Tanaka, I. / Harada, N. / Sano, K. / Kimura, M. / Yao, M. / Wakatsuki, S.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Study of the Ribosomal Protein S7 from Bacillus Stearothermophilus
Authors: Harada, N. / Sano, K. / Kimura, M. / Hosaka, H. / Nakagawa, A. / Tanaka, I.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S7


Theoretical massNumber of molelcules
Total (without water)18,2301
Polymers18,2301
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.400, 131.020, 29.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RIBOSOMAL PROTEIN S7


Mass: 18230.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: BL21 / Gene: S7 / Plasmid: BL21 / Gene (production host): S7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: P22744
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 8.2
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M NA HEPES BUFFER(PH8.2) WITH 4%(V/V) 2-PROPANOL AND 2.0M AMMONIUM SULFATE.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium HEPES11
24 %(v/v)2-propanol11
32.0 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.90007
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1997 / Details: COLLIMATING AND FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90007 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 7586 / % possible obs: 97.6 % / Observed criterion σ(I): 18.7 / Redundancy: 2.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.8 / % possible all: 92.9
Reflection
*PLUS
Num. measured all: 53236
Reflection shell
*PLUS
% possible obs: 92.9 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MAD WITH SE-MET MUTANT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFMAC (G.N.MURSHUDOV ET AL.) WAS ALSO USED DURING THE REFINEMENT CYCLE. PARAMETERS OF SE-MET WAS DERIVED FROM THOSE OF METHIONINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 715 9.8 %RANDOM
Rwork0.216 ---
obs0.216 7305 98 %-
Displacement parametersBiso mean: 33.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 0 25 1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it8.231.5
X-RAY DIFFRACTIONx_mcangle_it10.572
X-RAY DIFFRACTIONx_scbond_it11.452
X-RAY DIFFRACTIONx_scangle_it16.272.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.339 81 9.5 %
Rwork0.353 769 -
obs--93.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12

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