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- PDB-7z8a: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7z8a
TitleSam68
ComponentsKHDR1 protein
KeywordsRNA BINDING PROTEIN / STAR
Function / homology
Function and homology information


poly(A) binding / regulation of alternative mRNA splicing, via spliceosome / mRNA processing / mRNA binding / nucleus
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
: / NITRATE ION / S-1,2-PROPANEDIOL / KHDR1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsNadal, M. / Fuentes-Prior, P.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other private Spain
CitationJournal: Protein Sci. / Year: 2023
Title: Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts.
Authors: Nadal, M. / Anton, R. / Dorca-Arevalo, J. / Estebanez-Perpina, E. / Tizzano, E.F. / Fuentes-Prior, P.
History
DepositionMar 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: KHDR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,15718
Polymers13,1161
Non-polymers1,04217
Water86548
1
AAA: KHDR1 protein
hetero molecules

AAA: KHDR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31436
Polymers26,2312
Non-polymers2,08334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area7520 Å2
ΔGint1 kcal/mol
Surface area14180 Å2
Unit cell
Length a, b, c (Å)68.565, 68.565, 83.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein KHDR1 protein


Mass: 13115.519 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Khdrbs1, MELVER_R13249 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K8A7M1

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Non-polymers , 5 types, 65 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate 2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→48.53 Å / Num. obs: 12775 / % possible obs: 99.4 % / Redundancy: 9.1 % / CC1/2: 0.3 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 1402 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMO

5emo


Resolution: 2.06→48.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.346 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.151 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2464 625 4.892 %
Rwork0.2037 12150 -
all0.206 --
obs-12775 99.533 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.544 Å2
Baniso -1Baniso -2Baniso -3
1--1.562 Å20 Å20 Å2
2---1.562 Å20 Å2
3---3.124 Å2
Refinement stepCycle: LAST / Resolution: 2.06→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 68 48 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012989
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.6551302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58823.02343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77815186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.292154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02726
X-RAY DIFFRACTIONr_nbd_refined0.2340.2467
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6040.28
X-RAY DIFFRACTIONr_mcbond_it3.5943.742459
X-RAY DIFFRACTIONr_mcangle_it4.8885.599572
X-RAY DIFFRACTIONr_scbond_it7.744.921530
X-RAY DIFFRACTIONr_scangle_it10.9886.83730
X-RAY DIFFRACTIONr_lrange_it12.92374.5833845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1130.382500.373883X-RAY DIFFRACTION99.7861
2.113-2.1710.326360.326844X-RAY DIFFRACTION99.0991
2.171-2.2340.334440.334830X-RAY DIFFRACTION99.5444
2.234-2.3030.473400.344805X-RAY DIFFRACTION99.5289
2.303-2.3780.401370.272799X-RAY DIFFRACTION99.8805
2.378-2.4620.25450.242766X-RAY DIFFRACTION100
2.462-2.5550.247340.245737X-RAY DIFFRACTION99.7413
2.555-2.6590.258350.221700X-RAY DIFFRACTION99.4587
2.659-2.7770.275380.212696X-RAY DIFFRACTION100
2.777-2.9120.24340.203656X-RAY DIFFRACTION100
2.912-3.0690.22320.2623X-RAY DIFFRACTION100
3.069-3.2550.306280.187601X-RAY DIFFRACTION99.683
3.255-3.4790.203390.186556X-RAY DIFFRACTION99.1667
3.479-3.7570.233340.147514X-RAY DIFFRACTION99.8178
3.757-4.1140.169160.135496X-RAY DIFFRACTION99.2248
4.114-4.5980.133190.133454X-RAY DIFFRACTION99.3697
4.598-5.3050.196150.167406X-RAY DIFFRACTION99.0588
5.305-6.4880.269210.221334X-RAY DIFFRACTION98.0663
6.488-9.1350.219160.204275X-RAY DIFFRACTION98.3108
9.135-48.530.274120.236175X-RAY DIFFRACTION98.4211

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