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- PDB-3les: 2F5 Epitope scaffold ES2 -

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Basic information

Entry
Database: PDB / ID: 3les
Title2F5 Epitope scaffold ES2
ComponentsRNA polymerase sigma factor
KeywordsIMMUNE SYSTEM / HIV-1 / GP41 / MONOCLONAL ANTIBODY / 2F5 / EPITOPE / TRANSPLANT / SCAFFOLD / GRAFT / SIGMA FACTOR / RE-ELICITATION / VACCINE DESIGN
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsOfek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Wyatt, R. / Baker, D. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elicitation of structure-specific antibodies by epitope scaffolds.
Authors: Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 31, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor
B: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8036
Polymers40,4192
Non-polymers3844
Water50428
1
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4974
Polymers20,2091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3052
Polymers20,2091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.257, 49.987, 57.567
Angle α, β, γ (deg.)78.03, 89.83, 87.57
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 93:269 )
211chain B and (resseq 93:269 )

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Components

#1: Protein RNA polymerase sigma factor


Mass: 20209.309 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 93-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: SIGMA FACTOR SIGA / Plasmid: CMV-R / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9EZJ8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growDetails: 23% PEG 4000, 0.12 M (NH4)2SO4, 0.02 M ATP, VAPOR DIFFUSION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2005
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 9968 / % possible obs: 95.9 % / Observed criterion σ(I): 4 / Redundancy: 1.8 % / Biso Wilson estimate: 62.4 Å2 / Rsym value: 0.062 / Net I/σ(I): 15
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.49 / Rsym value: 0.411 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KU2
Resolution: 2.77→48.85 Å / SU ML: 0.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 909 10.3 %
Rwork0.227 --
obs0.23 8827 85.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.65 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 100.56 Å2
Baniso -1Baniso -2Baniso -3
1--28.79 Å27.1868 Å26.8682 Å2
2--48.8149 Å227.8848 Å2
3----20.0249 Å2
Refinement stepCycle: LAST / Resolution: 2.77→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 20 28 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042893
X-RAY DIFFRACTIONf_angle_d0.7513893
X-RAY DIFFRACTIONf_dihedral_angle_d16.8481100
X-RAY DIFFRACTIONf_chiral_restr0.05430
X-RAY DIFFRACTIONf_plane_restr0.003496
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1408X-RAY DIFFRACTIONPOSITIONAL
12B1408X-RAY DIFFRACTIONPOSITIONAL0.022
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.01060.0646-0.01180.0770.09510.1007-0.10040.09680.0023-0.0880.32640.07160.3190.309600.7520.1660.05130.64620.04720.692510.3711-3.03163.5373
20.05780.07360.1514-0.0664-0.06340.0834-0.1660.47620.1066-0.1602-0.02060.09510.08530.036-00.5195-0.0256-0.07490.86950.14770.5963-9.42391.282-4.3195
30.0122-0.00170.0180.0105-0.0486-0.01120.0251-0.13490.2166-0.00310.2605-0.0328-0.1562-0.1266-00.6476-0.1104-0.01090.94120.19380.5155-7.4462-8.79515.0849
40.2829-0.2139-0.26710.2037-0.17710.0852-0.04180.0178-0.05780.07990.1079-0.0909-0.1317-0.5265-00.60440.03750.00970.66230.01560.56470.99293.15176.0763
50.1172-0.10880.0730.00860.06210.003-0.0978-0.0193-0.22970.17760.17470.1302-0.0816-0.3005-00.71980.0154-0.02330.6388-0.07290.72016.371139.155134.7174
60.048-0.0273-0.0528-0.02940.10330.0332-0.1347-0.2366-0.11750.01240.0343-0.0634-0.00170.3463-00.55820.00360.0040.7485-0.02980.597425.791632.369329.2875
7-0.02170.0093-0.0127-0.0155-0.02510.0032-0.04950.21550.11110.05480.14680.11130.01550.091900.5692-0.060.0860.8789-0.08530.488324.482445.108334.4495
80.27560.0173-0.07490.14020.05460.0138-0.0263-0.0709-0.09390.08040.00890.0108-0.02090.2604-00.6115-0.00380.01220.4999-0.02880.594315.885934.553938.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 93:121
2X-RAY DIFFRACTION2chain A and resid 122:156
3X-RAY DIFFRACTION3chain A and resid 157:171
4X-RAY DIFFRACTION4chain A and resid 172:271
5X-RAY DIFFRACTION5chain B and resid 93:121
6X-RAY DIFFRACTION6chain B and resid 122:157
7X-RAY DIFFRACTION7chain B and resid 158:170
8X-RAY DIFFRACTION8chain B and resid 171:269

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