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- PDB-4glm: Crystal structure of the SH3 Domain of DNMBP protein [Homo sapiens] -

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Basic information

Entry
Database: PDB / ID: 4glm
TitleCrystal structure of the SH3 Domain of DNMBP protein [Homo sapiens]
ComponentsDynamin-binding protein
KeywordsSIGNALING PROTEIN / SH3 Domain / DNMBP / Structural Genomics / Structural Genomics Consortium / SGC / Src homology 3 domains / cell junctions / dynamin binding
Function / homology
Function and homology information


Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / cytoskeleton / intracellular signal transduction ...Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / cytoskeleton / intracellular signal transduction / synapse / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Dynamin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDong, A. / Guan, X. / Huang, H. / Tempel, W. / Gu, J. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the SH3 Domain of DNMBP protein [Homo sapiens]
Authors: Guan, X. / Dong, A. / Huang, H. / Tempel, W. / Gu, J. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-binding protein
B: Dynamin-binding protein
C: Dynamin-binding protein
D: Dynamin-binding protein


Theoretical massNumber of molelcules
Total (without water)31,00722
Polymers31,0074
Non-polymers018
Water2,432135
1
A: Dynamin-binding protein


Theoretical massNumber of molelcules
Total (without water)7,7529
Polymers7,7521
Non-polymers08
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dynamin-binding protein


Theoretical massNumber of molelcules
Total (without water)7,7527
Polymers7,7521
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dynamin-binding protein


Theoretical massNumber of molelcules
Total (without water)7,7524
Polymers7,7521
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dynamin-binding protein


Theoretical massNumber of molelcules
Total (without water)7,7522
Polymers7,7521
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.279, 136.203, 33.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein
Dynamin-binding protein / Scaffold protein Tuba


Mass: 7751.870 Da / Num. of mol.: 4 / Fragment: UNP residues 246-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMBP, KIAA1010 / Plasmid: pHH0239 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q6XZF7
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 5% PEG 8000, 0.2 M NaCl, and 0.1 M Tris 8.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21923 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.181 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.937.10.75710830.7631100
1.93-1.977.20.58210850.81100
1.97-2.017.40.55510580.8361100
2.01-2.057.50.44610580.854199.9
2.05-2.097.50.34811090.8891100
2.09-2.147.50.3310570.9151100
2.14-2.197.50.28210700.9221100
2.19-2.257.50.24810930.93199.8
2.25-2.327.60.22910550.9661100
2.32-2.397.50.18810930.9051100
2.39-2.487.60.17210800.944199.9
2.48-2.587.60.14511050.9591100
2.58-2.77.60.10810830.992199.9
2.7-2.847.60.09710821.0991100
2.84-3.027.60.08210891.4281100
3.02-3.257.50.07111141.8071100
3.25-3.587.60.06311082.251100
3.58-4.097.50.04711252.0881100
4.09-5.167.40.03211401.5361100
5.16-507.10.03112361.546199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DRK

2drk


Resolution: 1.9→35.82 Å / Cor.coef. Fo:Fc: 0.9312 / Cor.coef. Fo:Fc free: 0.9247 / Occupancy max: 1 / Occupancy min: 0.4 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 915 4.18 %RANDOM
Rwork0.2289 ---
obs0.2302 21876 99.77 %-
Displacement parametersBiso max: 145.16 Å2 / Biso mean: 40.3978 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.7184 Å20 Å20 Å2
2---7.8918 Å20 Å2
3---7.1734 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 18 135 1916
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2363 104 3.7 %
Rwork0.2049 2705 -
all0.2061 2809 -
obs--99.77 %
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)
13.3451-0.55872.3241.72230.07194.5338-0.03560.18070.1227-0.0046-0.0237-0.0274-0.29170.36470.0593-0.0276-0.0324-0.0065-0.03780.0194-0.062727.065440.8188-20.8125
23.4048-0.17852.19411.6127-0.64764.81330.0174-0.15540.10130.0057-0.022-0.0153-0.1937-0.41740.0046-0.05350.02710.0103-0.0188-0.0115-0.0634.063241.0008-29.9175
33.58320.36-0.8647.5495-0.27526.3453-0.01820.3139-0.0956-0.6721-0.5241-0.1778-0.8991-0.3760.54230.12910.21340.0143-0.18780.0098-0.17284.47256.9693-14.2518
42.57040.3661-1.856912.6771-2.20866.98850.0936-0.1927-0.04590.6266-0.4068-0.143-1.08450.75360.31320.093-0.198-0.0483-0.17820.0288-0.198225.785856.595-2.1684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A245 - 302
2X-RAY DIFFRACTION2{ B|* }B245 - 301
3X-RAY DIFFRACTION3{ C|* }C246 - 301
4X-RAY DIFFRACTION4{ D|* }D245 - 301

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