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- PDB-4rqn: Crystal structure of the native BICC1 SAM Domain R924E mutant -

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Basic information

Entry
Database: PDB / ID: 4rqn
TitleCrystal structure of the native BICC1 SAM Domain R924E mutant
ComponentsProtein bicaudal C homolog 1
KeywordsPROTEIN BINDING / SAM domain / protein-protein interaction domain / polymerization domain / Polymerization / P-bodies
Function / homology
Function and homology information


determination of left/right symmetry / kidney development / negative regulation of canonical Wnt signaling pathway / heart development / RNA binding / cytoplasm
Similarity search - Function
BICC1, SAM domain / : / : / : / Transcription Factor, Ets-1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) / K Homology domain, type 1 superfamily ...BICC1, SAM domain / : / : / : / Transcription Factor, Ets-1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) / K Homology domain, type 1 superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / K Homology domain / K homology RNA-binding domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein bicaudal C homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLeettola, C.N. / Cascio, D. / Bowie, J.U.
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.
Authors: Rothe, B. / Leettola, C.N. / Leal-Esteban, L. / Cascio, D. / Fortier, S. / Isenschmid, M. / Bowie, J.U. / Constam, D.B.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Protein bicaudal C homolog 1
B: Protein bicaudal C homolog 1
C: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3004
Polymers24,2353
Non-polymers651
Water28816
1
A: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1442
Polymers8,0781
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)8,0781
Polymers8,0781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)8,0781
Polymers8,0781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.680, 59.220, 68.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERASNASNchain AAA876 - 9368 - 68
2GLYGLYLYSLYSchain BBB875 - 9357 - 67
3ASPASPARGARGchain CCC877 - 9389 - 70

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Components

#1: Protein Protein bicaudal C homolog 1 / Bic-C


Mass: 8078.169 Da / Num. of mol.: 3 / Fragment: SAM domain of BICC1, UNP residues 870-939 / Mutation: R924E
Source method: isolated from a genetically manipulated source
Details: SER 869 is an artifact of cloning / Source: (gene. exp.) Homo sapiens (human) / Gene: BICC1 / Plasmid: pHis-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9H694
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.75 Å3/Da / Density % sol: 29.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG-550 MME, 100mM MES, 5mM zinc sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→59.22 Å / Num. all: 11813 / Num. obs: 11813 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 12.65 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 14.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.4864.38198.7
2.05-2.110.3895.87198.2
2.11-2.170.3167.03198.4
2.17-2.240.2748.28197.2
2.24-2.310.2369.97198.6
2.31-2.390.20411.89198.9
2.39-2.480.18313.43198.9
2.48-2.580.15715199
2.58-2.70.14115.86199.3
2.7-2.830.1217.86196.9
2.83-2.980.11619.35198.9
2.98-3.160.11121.02199.5
3.16-3.380.122.32199.6
3.38-3.650.09222.79199.4
3.65-40.09123.23199.8
4-4.470.08423.98195.4
4.47-5.160.0825.01199.7
5.16-6.320.08224.22199.7
6.32-8.940.08323.3193.5
8.94-59.220.0824.28198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.89 Å59.22 Å
Translation1.89 Å59.22 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RQM

4rqm


Resolution: 2→44.844 Å / SU ML: 0.23 / σ(F): 1.39 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 1179 9.98 %
Rwork0.2124 --
obs0.2175 11809 98.47 %
all-11809 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5015 Å2
Refinement stepCycle: LAST / Resolution: 2→44.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 1 16 1414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081412
X-RAY DIFFRACTIONf_angle_d1.0811905
X-RAY DIFFRACTIONf_dihedral_angle_d13.424509
X-RAY DIFFRACTIONf_chiral_restr0.045235
X-RAY DIFFRACTIONf_plane_restr0.006240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A802X-RAY DIFFRACTION6.459TORSIONAL
12B802X-RAY DIFFRACTION6.459TORSIONAL
13C802X-RAY DIFFRACTION6.459TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.28611420.22791292X-RAY DIFFRACTION98
2.091-2.20130.29171460.2211306X-RAY DIFFRACTION98
2.2013-2.33920.2671440.21481301X-RAY DIFFRACTION99
2.3392-2.51980.26311460.21631311X-RAY DIFFRACTION99
2.5198-2.77330.30711480.22491337X-RAY DIFFRACTION99
2.7733-3.17460.28811460.23751314X-RAY DIFFRACTION98
3.1746-3.99920.25461510.21231363X-RAY DIFFRACTION100
3.9992-44.85530.25041560.20081406X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 27.0157 Å / Origin y: 16.9117 Å / Origin z: 84.6974 Å
111213212223313233
T0.3771 Å2-0.0233 Å20.0033 Å2-0.3125 Å2-0.0586 Å2--0.3812 Å2
L0.5156 °20.0141 °20.006 °2-0.9959 °2-1.6049 °2--3.0982 °2
S0.0237 Å °0.0126 Å °-0.0323 Å °-0.0506 Å °0.0186 Å °0.0079 Å °0.0508 Å °-0.0775 Å °-0.038 Å °
Refinement TLS groupSelection details: all

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