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- PDB-4ld6: PWWP domain of human PWWP Domain-Containing Protein 2B -

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Basic information

Entry
Database: PDB / ID: 4ld6
TitlePWWP domain of human PWWP Domain-Containing Protein 2B
ComponentsPWWP domain-containing protein 2B
KeywordsUNKNOWN FUNCTION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of cold-induced thermogenesis / NuRD complex binding / positive regulation of transcription elongation by RNA polymerase II / chromatin remodeling / nucleoplasm / nucleus
Similarity search - Function
SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
PWWP domain-containing protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDong, A. / Dombrovski, L. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of PWWP domain of human PWWP Domain-Containing Protein 2B
Authors: Dombrovski, L. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PWWP domain-containing protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3568
Polymers13,2641
Non-polymers927
Water2,342130
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.148, 41.055, 77.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PWWP domain-containing protein 2B


Mass: 13264.072 Da / Num. of mol.: 1 / Fragment: PWWP domain (UNP residues 475-590)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PWWP2B, PWWP2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpRARE / References: UniProt: Q6NUJ5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.54178
SYNCHROTRONAPS 23-ID-B20.97944
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS HTC1IMAGE PLATEJun 7, 2013
MARMOSAIC 300 mm CCD2CCDJun 22, 2012Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1VariMaxSINGLE WAVELENGTHMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.979441
ReflectionResolution: 1.7→50 Å / Num. all: 11827 / Num. obs: 11827 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 56.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.7 / Num. unique all: 497 / % possible all: 87.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.841 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 660 5.6 %RANDOM
Rwork0.1679 ---
obs0.1694 11787 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.01 Å2 / Biso mean: 17.754 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.69 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 12 130 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191060
X-RAY DIFFRACTIONr_bond_other_d0.0010.021025
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9441450
X-RAY DIFFRACTIONr_angle_other_deg0.77432371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.12621.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1781512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02265
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 48 -
Rwork0.328 686 -
all-734 -
obs--87.28 %

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