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- PDB-1duq: CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1 -

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Basic information

Entry
Database: PDB / ID: 1duq
TitleCRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1
Components(THE REV BINDING ELEMENT) x 2
KeywordsRNA / RRE / HIV-1 / REV BINDING DOMAIN
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsHung, L.-W. / Holbrook, E.L. / Holbrook, S.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
Authors: Hung, L.W. / Holbrook, E.L. / Holbrook, S.R.
History
DepositionJan 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_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: THE REV BINDING ELEMENT
B: THE REV BINDING ELEMENT
C: THE REV BINDING ELEMENT
D: THE REV BINDING ELEMENT
E: THE REV BINDING ELEMENT
F: THE REV BINDING ELEMENT
G: THE REV BINDING ELEMENT
H: THE REV BINDING ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,76618
Polymers33,5368
Non-polymers23010
Water1,49583
1
A: THE REV BINDING ELEMENT
B: THE REV BINDING ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4073
Polymers8,3842
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: THE REV BINDING ELEMENT
D: THE REV BINDING ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4766
Polymers8,3842
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: THE REV BINDING ELEMENT
F: THE REV BINDING ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4073
Polymers8,3842
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: THE REV BINDING ELEMENT
H: THE REV BINDING ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4766
Polymers8,3842
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.993, 53.930, 64.729
Angle α, β, γ (deg.)114.52, 89.88, 102.85
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: RNA chain
THE REV BINDING ELEMENT


Mass: 3922.400 Da / Num. of mol.: 4 / Fragment: SHORT CHAIN / Source method: obtained synthetically / Details: SEQUENCE FROM HIV-1. SYNTHESIZED BY OLIGOS, ETC.
#2: RNA chain
THE REV BINDING ELEMENT


Mass: 4461.723 Da / Num. of mol.: 4 / Fragment: LONG CHAIN / Source method: obtained synthetically
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE, PH 6.5, 0.2 M NACL, 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2NACL11
3MPD11
4MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 mMEDTA1drop
22 mMprotein1drop
30.1 Msodium cacodylate1reservoir
40.2 M1reservoirNaCl
535 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 16703 / Num. obs: 15998 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.248 / % possible all: 83.2
Reflection shell
*PLUS
% possible obs: 83 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→19.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 659115.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1431 10.1 %RANDOM
Rwork0.218 ---
all0.221 15998 --
obs0.218 14136 84.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.11 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.52 Å20.39 Å2-0.73 Å2
2---3.54 Å22.74 Å2
3----4.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2220 10 83 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
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 shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 177 10.1 %
Rwork0.301 1581 -
obs--62.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA_REP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57
LS refinement shell
*PLUS
Rfactor Rfree: 0.385 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.301

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