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- PDB-3pa6: Structure of the N-terminal BRCT domain of human microcephalin (MCPH1) -

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Basic information

Entry
Database: PDB / ID: 3pa6
TitleStructure of the N-terminal BRCT domain of human microcephalin (MCPH1)
ComponentsMicrocephalin
KeywordsCELL CYCLE / BRCT DOMAIN
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / cerebral cortex development / mitotic cell cycle / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding
Similarity search - Function
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSingh, N. / Heroux, A. / Thompson, J.R. / Mer, G.
CitationJournal: To be Published
Title: Structure of the N-terminal BRCT domain of human microcephalin (MCPH1)
Authors: Singh, N. / Heroux, A. / Thompson, J.R. / Mer, G.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Microcephalin
B: Microcephalin
C: Microcephalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2974
Polymers36,2623
Non-polymers351
Water5,639313
1
A: Microcephalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1232
Polymers12,0871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microcephalin


Theoretical massNumber of molelcules
Total (without water)12,0871
Polymers12,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Microcephalin


Theoretical massNumber of molelcules
Total (without water)12,0871
Polymers12,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.069, 39.274, 106.639
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microcephalin


Mass: 12087.342 Da / Num. of mol.: 3 / Fragment: BRCT DOMAIN, UNP residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pGB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 295 K / pH: 7
Details: 0.2M sodium succinate, 15% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979095
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2008
RadiationMonochromator: SI(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979095 Å / Relative weight: 1
ReflectionResolution: 1.5→35.53 Å / Num. obs: 41554 / % possible obs: 88.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 46.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.9 / % possible all: 43.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→35.53 Å / SU ML: 0.15 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 2032 4.89 %
Rwork0.144 --
obs0.146 41554 88.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.52 Å2 / ksol: 0.5 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6965 Å20 Å2-4.1618 Å2
2--2.0072 Å20 Å2
3----11.382 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 1 313 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132386
X-RAY DIFFRACTIONf_angle_d1.3393249
X-RAY DIFFRACTIONf_dihedral_angle_d13.97871
X-RAY DIFFRACTIONf_chiral_restr0.08372
X-RAY DIFFRACTIONf_plane_restr0.008403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.55460.2762820.23151800X-RAY DIFFRACTION41
1.5546-1.61690.21431180.19622794X-RAY DIFFRACTION63
1.6169-1.69050.22021810.17073797X-RAY DIFFRACTION85
1.6905-1.77960.20542140.15514383X-RAY DIFFRACTION99
1.7796-1.89110.19272360.14214403X-RAY DIFFRACTION100
1.8911-2.03710.20682350.11614421X-RAY DIFFRACTION100
2.0371-2.24220.17332510.11554403X-RAY DIFFRACTION100
2.2422-2.56660.1922510.11894436X-RAY DIFFRACTION100
2.5666-3.23370.19622040.13024530X-RAY DIFFRACTION100
3.2337-106.87130.17422600.15524555X-RAY DIFFRACTION100

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