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- PDB-2wt8: Structure of the N-terminal BRCT domain of human microcephalin (Mcph1) -

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Basic information

Entry
Database: PDB / ID: 2wt8
TitleStructure of the N-terminal BRCT domain of human microcephalin (Mcph1)
ComponentsMICROCEPHALIN
KeywordsCELL CYCLE / CHROMOSOME CONDENSATION / DWARFISM / POLYMORPHISM / MICROCEPHALY / PHOSPHOPROTEIN / MENTAL RETARDATION / PRIMARY MICROCEPHALY
Function / homology
Function and homology information


regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / protein localization to centrosome / establishment of mitotic spindle orientation / Condensation of Prophase Chromosomes / bone development / cerebral cortex development / mitotic cell cycle / regulation of inflammatory response ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / protein localization to centrosome / establishment of mitotic spindle orientation / Condensation of Prophase Chromosomes / bone development / cerebral cortex development / mitotic cell cycle / regulation of inflammatory response / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm
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
ACETATE ION / Microcephalin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsRichards, M.W. / Roe, S.M. / Bayliss, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Pocket on the Surface of the N-Terminal Brct Domain of Mcph1 is Required to Prevent Abnormal Chromosome Condensation.
Authors: Richards, M.W. / Leung, J.W.C. / Roe, S.M. / Chen, J. / Bayliss, R.
History
DepositionSep 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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
D: MICROCEPHALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4267
Polymers43,2724
Non-polymers1543
Water8,449469
1
A: MICROCEPHALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9133
Polymers10,8181
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MICROCEPHALIN


Theoretical massNumber of molelcules
Total (without water)10,8181
Polymers10,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MICROCEPHALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8772
Polymers10,8181
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MICROCEPHALIN


Theoretical massNumber of molelcules
Total (without water)10,8181
Polymers10,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.955, 34.215, 84.230
Angle α, β, γ (deg.)90.00, 113.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MICROCEPHALIN


Mass: 10818.010 Da / Num. of mol.: 4 / Fragment: N-TERMINAL BRCT DOMAIN, RESIDUES 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): CODONPLUS RPIL / References: UniProt: Q8NEM0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL GA FROM VECTOR SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 % / Description: NONE
Crystal growDetails: 100 MM MES, PH 6.0, 18% PEG 6000, 200 MM NH4CL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→45.27 Å / Num. obs: 56453 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 19.66 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→45.248 Å / SU ML: 0.24 / σ(F): 0.01 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2771 5.1 %
Rwork0.1902 --
obs0.1918 54743 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.822 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 28.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.0614 Å2-0 Å21.7023 Å2
2---2.4975 Å20 Å2
3----4.1416 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 9 469 3425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073027
X-RAY DIFFRACTIONf_angle_d1.0574105
X-RAY DIFFRACTIONf_dihedral_angle_d16.1751055
X-RAY DIFFRACTIONf_chiral_restr0.074469
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.28831090.23442445X-RAY DIFFRACTION90
1.6276-1.65720.27921470.22132376X-RAY DIFFRACTION91
1.6572-1.68910.23391350.20982440X-RAY DIFFRACTION92
1.6891-1.72360.24591360.20752475X-RAY DIFFRACTION93
1.7236-1.76110.30881310.21042492X-RAY DIFFRACTION95
1.7611-1.8020.24321380.19432557X-RAY DIFFRACTION95
1.802-1.84710.20491240.18542521X-RAY DIFFRACTION95
1.8471-1.8970.21691230.18942613X-RAY DIFFRACTION96
1.897-1.95290.22831450.19012561X-RAY DIFFRACTION97
1.9529-2.01590.21711450.18122633X-RAY DIFFRACTION98
2.0159-2.08790.20671360.17532590X-RAY DIFFRACTION98
2.0879-2.17150.21541380.17592663X-RAY DIFFRACTION99
2.1715-2.27040.25271450.18332673X-RAY DIFFRACTION99
2.2704-2.39010.2071390.19482634X-RAY DIFFRACTION99
2.3901-2.53980.21081460.19312644X-RAY DIFFRACTION99
2.5398-2.73590.24791370.1992706X-RAY DIFFRACTION100
2.7359-3.01110.23061540.19852694X-RAY DIFFRACTION100
3.0111-3.44670.22461350.18732726X-RAY DIFFRACTION100
3.4467-4.34190.17841490.16072732X-RAY DIFFRACTION100
4.3419-45.26630.19151590.17772797X-RAY DIFFRACTION99
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)
10.90410.40310.08851.36290.25581.68120.00960.09340.081-0.0002-0.00660.09750.04620.043-0.01430.03180.0162-0.00020.0775-0.00120.085751.1641-2.53653.0511
21.4172-0.9849-0.57281.52520.48961.8120.0604-0.12210.0156-0.1139-0.0048-0.1268-0.06510.0257-0.05350.0784-0.00090.00140.11080.01020.150769.484214.3632-1.9077
35.3715-2.3746-0.59522.23070.24621.8571-0.4252-0.3251-0.0540.03360.3755-0.0867-0.1634-0.02450.04690.22820.04590.01310.1363-0.02560.11546.612713.180330.7677
41.38280.0983-1.01720.48070.14872.59-0.03260.0150.05160.07320.0208-0.0816-0.1313-0.07060.00590.2772-0.0228-0.00030.1377-0.00460.163191.229812.77629.7056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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