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- PDB-1duh: CRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA -

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Basic information

Entry
Database: PDB / ID: 1duh
TitleCRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA
Components4.5S RNA DOMAIN IV
KeywordsRNA / 4.5S RNA / DOMAIN IV / HELIX 8 / SIGNAL RECOGNITION PARTICLE / SRP / FFH / SRP54 / ELONGATION FACTOR G / EF-G / 23S RNA / NON-CANONICAL BASE PAIRS / MISMATCH
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJovine, L. / Hainzl, T. / Oubridge, C. / Scott, W.G. / Li, J. / Sixma, T.K. / Wonacott, A. / Skarzynski, T. / Nagai, K.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
Authors: Jovine, L. / Hainzl, T. / Oubridge, C. / Scott, W.G. / Li, J. / Sixma, T.K. / Wonacott, A. / Skarzynski, T. / Nagai, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of the conserved domain IV of E. coli 4.5S RNA
Authors: Jovine, L. / Hainzl, T. / Oubridge, C. / Nagai, K.
History
DepositionJan 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: 4.5S RNA DOMAIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0555
Polymers14,6641
Non-polymers3914
Water1086
1
A: 4.5S RNA DOMAIN IV
hetero molecules

A: 4.5S RNA DOMAIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,11010
Polymers29,3272
Non-polymers7838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)69.697, 69.697, 84.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: RNA chain 4.5S RNA DOMAIN IV


Mass: 14663.736 Da / Num. of mol.: 1 / Fragment: DOMAIN IV / Source method: obtained synthetically
Details: RNA SEQUENCE TAKEN FROM ESCHERICHIA COLI 4.5S RNA. THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY
References: EMBL: X01074
#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Lu
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.15 Å3/Da / Density % sol: 76.9 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: CRYSTALLIZED FROM 1.60-1.90 M (NH4)2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION OF 2.20 M (NH4)2SO4, 0.01 M ...Details: CRYSTALLIZED FROM 1.60-1.90 M (NH4)2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION OF 2.20 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M BIS-TRIS-HCL PH 6.0. SOAK CONDITIONS: CRYSTALS WERE SOAKED IN STABILISATION SOLUTION CONTAINING 0.002 M LUTETIUM CHLORIDE HEXAHYDRATE. CRYOPROTECTION CONDITIONS: AFTER ADDITION OF 20% GLYCEROL (W/V) TO THE SOAK SOLUTION, CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN., VAPOR DIFFUSION, SITTING DROP, temperature 303.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2SODIUM CACODYLATE11
3BIS-TRIS-HCL11
4(NH4)2SO411
5MGCL211
6LUCL311
7(NH4)2SO412
8BIS-TRIS-HCL12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6-1.8 Mammonium sulfate1reservoir
290 mM1reservoirMg(OAc)2
350 mMNa cacodylate1reservoir
42 mM1reservoirCoNH36
51
61
71
81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0302, 1.3366, 1.3369, 0.9968, 1.3359
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03021
21.33661
31.33691
40.99681
51.33591
ReflectionResolution: 2.7→22.5 Å / Num. all: 12371 / Num. obs: 12371 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 100.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.1 / % possible all: 100
Reflection
*PLUS
Num. measured all: 154595
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→22.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1101782.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
Details: A LOW RESOLUTION LIMIT OF 8.0 A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. NUCLEOTIDE A39 WAS REFINED WITH OCCUPANCY OF 0.5 TO ACCOUNT FOR ITS ALTERNATIVELY ORDERED AND ...Details: A LOW RESOLUTION LIMIT OF 8.0 A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. NUCLEOTIDE A39 WAS REFINED WITH OCCUPANCY OF 0.5 TO ACCOUNT FOR ITS ALTERNATIVELY ORDERED AND DISORDERED CONFORMATION IN ADJACENT MOLECULES WITHIN THE CRYSTAL. THE APPARENT DISCREPANCY BETWEEN DATA COMPLETENESS IN SCALING AND REFINEMENT IS DUE TO THE VERY HIGH ANISOTROPY OF THE CRYSTAL DIFFRACTION, SO THAT, ALTHOUGH DATA COVERAGE WAS COMPLETE UP TO 2.70 A RESOLUTION, A SIGNIFICANT PROPORTION OF REFLECTIONS AT HIGH RESOLUTION WERE EXTINCT. THIS RESULTS IN THE HIGH R SYM IN THE OUTER SHELL, AND THE LOWER EFFECTIVE DATA COMPLETENESS DURING REFINEMENT (EXTINCT REFLECTIONS WERE OMITTED BY CNS).
RfactorNum. reflection% reflectionSelection details
Rfree0.245 909 8.6 %RANDOM
Rwork0.23 ---
all0.271 12560 --
obs0.244 10539 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.81 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso mean: 80.6 Å2
Baniso -1Baniso -2Baniso -3
1-26.51 Å221.46 Å20 Å2
2--26.51 Å20 Å2
3----53.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.9 Å0.92 Å
Refinement stepCycle: LAST / Resolution: 2.7→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 970 12 6 988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.7-2.820.531865.50.5318580.05760
2.82-2.970.4371066.80.43710220.04272.3
2.97-3.160.3641197.50.36311500.03380.4
3.16-3.40.3121177.50.31212920.02989.7
3.4-3.740.25110870.25112870.02489.9
3.74-4.290.2291328.40.22912950.0291.1
4.29-5.40.1761147.20.17614170.01697
5.4-60.360.15412580.15513000.01490.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA_RNA_REP+.PARAMDNA_RNA+.TOP
X-RAY DIFFRACTION2ION_REP+.PARAMION+.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP

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