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- PDB-3feo: The crystal structure of MBTD1 -

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Basic information

Entry
Database: PDB / ID: 3feo
TitleThe crystal structure of MBTD1
ComponentsMBT domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / MBTL1 / Structural Genomics / Structural Genomics Consortium / SGC / Metal-binding / Nucleus / Zinc-finger
Function / homology
Function and homology information


NuA4 histone acetyltransferase complex binding / embryonic skeletal system development / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / double-strand break repair via homologous recombination / nucleosome / site of double-strand break / chromatin organization ...NuA4 histone acetyltransferase complex binding / embryonic skeletal system development / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / double-strand break repair via homologous recombination / nucleosome / site of double-strand break / chromatin organization / regulation of apoptotic process / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SH3 type barrels. ...Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
MBT domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAmaya, M.F. / Eryilmaz, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2009
Title: Structural studies of a four-MBT repeat protein MBTD1.
Authors: Eryilmaz, J. / Pan, P. / Amaya, M.F. / Allali-Hassani, A. / Dong, A. / Adams-Cioaba, M.A. / Mackenzie, F. / Vedadi, M. / Min, J.
History
DepositionNov 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBT domain-containing protein 1
B: MBT domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)99,1312
Polymers99,1312
Non-polymers00
Water1,27971
1
A: MBT domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)49,5661
Polymers49,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MBT domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)49,5661
Polymers49,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.310, 100.904, 135.303
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 MBT domain-containing protein 1


Mass: 49565.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05BQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M CaOAc, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorDate: Nov 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 34002 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Χ2: 1.529 / Net I/σ(I): 26.317
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.595.30.40531551.32193.1
2.59-2.696.10.34332831.274197.7
2.69-2.826.80.29233941.331199.7
2.82-2.967.30.24333631.3981100
2.96-3.157.40.1734071.4521100
3.15-3.397.40.11234141.5131100
3.39-3.737.40.08334111.6081100
3.73-4.277.30.06634312.021100
4.27-5.397.30.05134911.8421100
5.39-1006.90.03436531.374199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F70

3f70


Resolution: 2.5→80.85 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 20.504 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.497 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1722 5.1 %RANDOM
Rwork0.207 ---
obs0.211 33927 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.15 Å2 / Biso mean: 21.071 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--3.42 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 0 71 6273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226409
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9298750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4322.62271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42215898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5161536
X-RAY DIFFRACTIONr_chiral_restr0.1190.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024978
X-RAY DIFFRACTIONr_nbd_refined0.2280.22603
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.26
X-RAY DIFFRACTIONr_mcbond_it0.9051.54098
X-RAY DIFFRACTIONr_mcangle_it1.47326415
X-RAY DIFFRACTIONr_scbond_it2.47132732
X-RAY DIFFRACTIONr_scangle_it3.5054.52335
LS refinement shellResolution: 2.5→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 122 -
Rwork0.309 2137 -
all-2259 -
obs--90.29 %
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)
10.4157-0.3976-0.79571.18990.62084.0622-0.09280.0218-0.1128-0.14510.00560.01650.27630.16450.08720.01040.0061-0.00860.0285-0.01580.00673.36917.3651-58.1456
22.73610.49350.78092.0318-0.30273.30130.01150.0678-0.2103-0.10330.0550.22460.1433-0.1986-0.0665-0.0285-0.03630.00120.01740.01870.0642-11.79742.3319-22.5047
30.79950.12910.3360.70140.08852.74670.0038-0.02960.01480.078-0.04440.054-0.0258-0.02010.0406-0.0485-0.00260.01610.0362-0.02530.00370.970918.3876-21.3528
40.22260.19440.46540.2791.19066.60370.03550.2068-0.0335-0.1273-0.0981-0.05920.1404-0.01150.0626-0.00670.05510.01970.2024-0.0022-0.01227.435714.7575-54.8587
50.57080.50141.02721.43421.53292.4646-0.1120.23390.0961-0.20090.0318-0.1811-0.3210.24260.0802-0.0066-0.05530.03960.07460.10280.066636.745930.3974-45.1117
61.1136-0.0340.37420.95440.51862.6640.00550.12420.09640.0875-0.0279-0.03570.01980.17120.0224-0.0565-0.0105-0.00050.00990.0354-0.006530.217723.3853-22.7047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 151
2X-RAY DIFFRACTION2A152 - 253
3X-RAY DIFFRACTION3A254 - 432
4X-RAY DIFFRACTION4B12 - 92
5X-RAY DIFFRACTION5B93 - 247
6X-RAY DIFFRACTION6B254 - 431

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