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- PDB-2qb1: 2TEL crystallization module -

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Basic information

Entry
Database: PDB / ID: 2qb1
Title2TEL crystallization module
ComponentsE80-TELSAM domain
KeywordsHYDROLASE REGULATOR / 2TEL helical polymer
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsNauli, S. / Bowie, J.U.
CitationJournal: Protein Sci. / Year: 2007
Title: Polymer-driven crystallization.
Authors: Nauli, S. / Farr, S. / Lee, Y.J. / Kim, H.Y. / Faham, S. / Bowie, J.U.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jun 24, 2020Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E80-TELSAM domain
B: E80-TELSAM domain


Theoretical massNumber of molelcules
Total (without water)18,2992
Polymers18,2992
Non-polymers00
Water724
1
A: E80-TELSAM domain


Theoretical massNumber of molelcules
Total (without water)9,1491
Polymers9,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E80-TELSAM domain


Theoretical massNumber of molelcules
Total (without water)9,1491
Polymers9,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.686, 65.686, 36.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 15 - 90 / Label seq-ID: 1 - 76

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsNot a biological assembly. This is a fusion protein of two naturally occurring proteins that makes a helical polymer.

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Components

#1: Protein E80-TELSAM domain


Mass: 9149.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 0.3M MnCl2, 0.1M sodium acetate , pH 5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→90 Å / Num. obs: 5306 / % possible obs: 99 % / Rmerge(I) obs: 0.092 / Χ2: 0.992 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.690.47110371.099198.2
2.69-2.80.28310770.9061100
2.8-2.930.21810300.9991100
2.93-3.080.16710941.0041100
3.08-3.280.13610990.93199.9
3.28-3.530.1210251.043198.3
3.53-3.880.110361.043198.2
3.88-4.450.0810700.982198.7
4.45-5.60.06710410.968199.9
5.6-900.06610551.011197.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.61 Å30.51 Å
Translation2.61 Å30.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI7

1ji7


Resolution: 2.61→56.89 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 30.244 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 242 4.6 %RANDOM
Rwork0.211 ---
obs0.212 5272 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.61→56.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 4 1298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211330
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9491808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4335154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23523.52968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.651510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021020
X-RAY DIFFRACTIONr_nbd_refined0.2260.2537
X-RAY DIFFRACTIONr_nbtor_refined0.310.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.26
X-RAY DIFFRACTIONr_mcbond_it4.1422804
X-RAY DIFFRACTIONr_mcangle_it5.41931256
X-RAY DIFFRACTIONr_scbond_it4.0112616
X-RAY DIFFRACTIONr_scangle_it5.7353552
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 633 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.010.05
TIGHT THERMAL0.040.5
LS refinement shellResolution: 2.61→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.569 25 -
Rwork0.398 352 -
obs-377 97.67 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.6088-5.47772.996412.0323-4.5822.42260.1305-0.4748-0.9224-0.5229-0.01920.37110.2375-0.005-0.11140.1063-0.0638-0.05530.12160.07970.0383-19.1336-4.77274.9615
27.1582.038-1.560417.0852-4.36322.6394-0.45910.079-0.15330.16110.6130.9550.1942-0.2355-0.15390.07020.04930.06170.14940.08840.0329-13.7048-23.764716.9909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 911 - 77
2X-RAY DIFFRACTION2BB15 - 911 - 77

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