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- PDB-3ob9: Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom ... -

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Basic information

Entry
Database: PDB / ID: 3ob9
TitleStructure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution
ComponentsMale-specific lethal 3-like 1 (Drosophila), isoform CRA_c
KeywordsTranscription Regulator / chromodomain / chromo-barrel / chromo / methyllysine binding / histone tail / nucleosome recognition / Histone H4K20Me1 / nucleus
Function / homology
Function and homology information


MSL complex / histone H4K16ac reader activity / NuA4 histone acetyltransferase complex / histone reader activity / HATs acetylate histones / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain ...: / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
MSL complex subunit 3 / MSL complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMoore, S.A. / Ferhatoglu, Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution
Authors: Moore, S.A. / Ferhatoglu, Y.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

Downloads & links

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Assembly

Deposited unit
A: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
B: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
C: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
D: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
E: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,41425
Polymers56,1595
Non-polymers2,25520
Water1,02757
1
A: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8236
Polymers11,2321
Non-polymers5925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7275
Polymers11,2321
Non-polymers4954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9048
Polymers11,2321
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5353
Polymers11,2321
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4243
Polymers11,2321
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.178, 36.696, 85.574
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c / Protein MSL3


Mass: 11231.825 Da / Num. of mol.: 5 / Fragment: hmsl3 (UNP residues 2 to 93)
Source method: isolated from a genetically manipulated source
Details: Bam HI/Eco RI MCS / Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_401190, MSL3, MSL3L1 / Plasmid: PGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A6NHW8, UniProt: Q8N5Y2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0 Ammonium Sulfate, 100 mM CHES pH 9.0, , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2009 / Details: Si 111 monochromator and focusing mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 19711 / Num. obs: 19514 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 56.7 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F5K

2f5k


Resolution: 2.5→29.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.713 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27726 997 5.1 %RANDOM
Rwork0.22564 ---
obs0.22823 18515 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.605 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å20 Å22.09 Å2
2--1.35 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 124 57 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223743
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9625061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43922.381189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28815624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9611542
X-RAY DIFFRACTIONr_chiral_restr0.0780.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212818
X-RAY DIFFRACTIONr_mcbond_it0.3881.52178
X-RAY DIFFRACTIONr_mcangle_it0.76323475
X-RAY DIFFRACTIONr_scbond_it1.20431565
X-RAY DIFFRACTIONr_scangle_it1.9694.51586
LS refinement shellResolution: 2.504→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 60 -
Rwork0.271 1219 -
obs--100 %
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)
14.25750.56130.4972.6084-0.42992.40050.0184-0.38480.07730.12620.03920.0542-0.0185-0.1605-0.05760.04360.006-0.01620.080.01820.036819.79741.00811.2151
25.9644-0.69061.7953.3046-0.1375.1985-0.0964-0.2763-0.00850.05960.19880.0489-0.0307-0.2245-0.10240.0448-0.00040.03790.0279-0.00350.048638.608311.83719.545
35.0315-1.5673-0.32153.95182.01365.1724-0.00490.2598-0.22250.0886-0.03760.04940.11910.07390.04250.0228-0.0093-0.01020.1554-0.05580.12614.5698-6.1199-13.2127
41.81340.22771.0232.37861.25944.37580.03610.14040.1489-0.1098-0.14730.1807-0.1229-0.23620.11120.11470.03520.00750.10450.00070.055225.4216-10.1604-20.5115
54.018-0.8751-3.14751.88720.33869.1091-0.07110.2345-0.13260.02070.08030.14990.1403-0.3537-0.00920.29690.0495-0.03730.1676-0.07690.144630.494110.579839.7606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 93
2X-RAY DIFFRACTION2B6 - 92
3X-RAY DIFFRACTION3C5 - 92
4X-RAY DIFFRACTION4D0 - 92
5X-RAY DIFFRACTION5E8 - 92

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