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- PDB-1jo0: Structure of HI1333, a Hypothetical Protein from Haemophilus infl... -

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Basic information

Entry
Database: PDB / ID: 1jo0
TitleStructure of HI1333, a Hypothetical Protein from Haemophilus influenzae with Structural Similarity to RNA-binding Proteins
ComponentsHYPOTHETICAL PROTEIN HI1333Hypothesis
KeywordsSTRUCTURAL GENOMICS / unknown function / hypothetical protein / HI1333 / YHBY_HAEIN / Structure 2 Function Project / S2F
Function / homology
Function and homology information


YhbY-like / RNA-binding, CRM domain / RNA-binding protein YhbY / YhbY-like superfamily / CRS1 / YhbY (CRM) domain / CRM domain profile. / CRS1_YhbY / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein HI_1333
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD (PT, BR) / Resolution: 1.37 Å
AuthorsWillis, M.A. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2002
Title: Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae
Authors: Willis, M.A. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Herzberg, O.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HYPOTHETICAL PROTEIN HI1333
B: HYPOTHETICAL PROTEIN HI1333
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2669
Polymers21,6212
Non-polymers6457
Water4,756264
1
A: HYPOTHETICAL PROTEIN HI1333
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1795
Polymers10,8111
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYPOTHETICAL PROTEIN HI1333
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0874
Polymers10,8111
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.566, 51.941, 59.100
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDynamic Light Scattering (DLS) indicates the protein is a monomer in solution. There are two monomers in the asymmetric unit.

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Components

#1: Protein HYPOTHETICAL PROTEIN HI1333 / Hypothesis


Mass: 10810.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI1333 / Plasmid: pRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): MZ1 / References: UniProt: P71376
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.77 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28-30% PEG4000, 100mM Tris pH 8.0, 10mM CaCl2, + 1.5% heptane-1,2,3-triol added to drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium phosphate11pH7.0
2100 mM11NaCl
318 mg/mlprotein12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9184 / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2001 / Details: PT/PD-COATED ULE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.37→25.9 Å / Num. all: 38052 / Num. obs: 38052 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.47 % / Rmerge(I) obs: 0.0308 / Net I/σ(I): 26.79
Reflection shellResolution: 1.37→1.4 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.2705 / Mean I/σ(I) obs: 3.06 / Num. unique all: 2391 / % possible all: 100
Reflection
*PLUS
Num. obs: 38069 / Num. measured all: 246633 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Lowest resolution: 1.42 Å / % possible obs: 100 % / Rmerge(I) obs: 0.271

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Processing

Software
NameVersionClassification
SHELXL-97refinement
SCALEPACK1.96.1data scaling
XPREP6.09data reduction
SOLVEphasing
RESOLVEmodel building
CNSrefinement
SHELXmodel building
DENZO1.96.1data reduction
RESOLVEphasing
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MAD (PT, BR) / Resolution: 1.37→25.9 Å / Num. parameters: 16757 / Num. restraintsaints: 20338 / Cross valid method: FREE R / σ(I): -3 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 3072 8.07 %RANDOM
Rwork0.1379 ---
all-38052 --
obs-38052 99.9 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 1525 / Occupancy sum non hydrogen: 1771.5
Refinement stepCycle: LAST / Resolution: 1.37→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 42 264 1795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0.093
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 8 % / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.058
LS refinement shell
*PLUS
Rfactor Rfree: 0.213 / Rfactor Rwork: 0.132

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