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- PDB-2ek1: Crystal structure of RNA-binding motif of human rna-binding protein 12 -

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Basic information

Entry
Database: PDB / ID: 2ek1
TitleCrystal structure of RNA-binding motif of human rna-binding protein 12
ComponentsRNA-binding protein 12
KeywordsRNA BINDING PROTEIN / RNA recognition motif / dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of RNA splicing / ribonucleoprotein complex / RNA binding / nucleoplasm
Similarity search - Function
RBM12, RNA recognition motif 1 / RBM12, RNA recognition motif 2 / RBM12, RNA recognition motif 5 / RBM12, RNA recognition motif 3 / RBM12, RNA recognition motif 4 / : / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...RBM12, RNA recognition motif 1 / RBM12, RNA recognition motif 2 / RBM12, RNA recognition motif 5 / RBM12, RNA recognition motif 3 / RBM12, RNA recognition motif 4 / : / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsIhsanawati / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of RNA-binding motif of human rna-binding protein 12
Authors: Ihsanawati / Bessho, Y. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 12
B: RNA-binding protein 12
C: RNA-binding protein 12
D: RNA-binding protein 12
E: RNA-binding protein 12
F: RNA-binding protein 12
G: RNA-binding protein 12
H: RNA-binding protein 12


Theoretical massNumber of molelcules
Total (without water)80,5438
Polymers80,5438
Non-polymers00
Water7,909439
1
A: RNA-binding protein 12
B: RNA-binding protein 12


Theoretical massNumber of molelcules
Total (without water)20,1362
Polymers20,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9.8 kcal/mol
Surface area8470 Å2
MethodPISA
2
C: RNA-binding protein 12
D: RNA-binding protein 12


Theoretical massNumber of molelcules
Total (without water)20,1362
Polymers20,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-9.8 kcal/mol
Surface area8690 Å2
MethodPISA
3
E: RNA-binding protein 12
F: RNA-binding protein 12


Theoretical massNumber of molelcules
Total (without water)20,1362
Polymers20,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9.5 kcal/mol
Surface area8580 Å2
MethodPISA
4
G: RNA-binding protein 12
H: RNA-binding protein 12


Theoretical massNumber of molelcules
Total (without water)20,1362
Polymers20,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10.5 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.879, 103.227, 62.189
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA-binding protein 12 / RRM / RNA-binding motif protein 12 / SH3/WW domain anchor protein in the nucleus / SWAN


Mass: 10067.821 Da / Num. of mol.: 8 / Fragment: residues 861-955
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell Free system / Gene: RBM12, KIAA0765 / Plasmid: PX041122-21 / References: UniProt: Q9NTZ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 25% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97947, 0.97964, 0.964
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.979641
30.9641
ReflectionResolution: 2→30 Å / Num. obs: 39769 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.102
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.312 / % possible all: 89.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1922580.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1988 5 %RANDOM
Rwork0.208 ---
obs0.208 39675 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3441 Å2 / ksol: 0.322088 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å2-2.15 Å2
2---3.21 Å20 Å2
3----0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4827 0 0 439 5266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.72
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 297 4.8 %
Rwork0.23 5918 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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