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- PDB-3uun: Crystal Structure of N-terminal first spectrin repeat of dystrophin -

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Basic information

Entry
Database: PDB / ID: 3uun
TitleCrystal Structure of N-terminal first spectrin repeat of dystrophin
ComponentsDystrophin
KeywordsSTRUCTURAL PROTEIN / triple helical / Cell structure and stability / Cytoskeletal
Function / homology
Function and homology information


regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / regulation of voltage-gated calcium channel activity / negative regulation of peptidyl-cysteine S-nitrosylation / positive regulation of sodium ion transmembrane transporter activity / dystrophin-associated glycoprotein complex / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / peptide biosynthetic process / cell-substrate junction / motile cilium assembly / dystroglycan binding / vinculin binding / muscle cell development / costamere / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / muscle organ development / structural constituent of muscle / muscle cell cellular homeostasis / maintenance of blood-brain barrier / myosin binding / nitric-oxide synthase binding / Non-integrin membrane-ECM interactions / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / negative regulation of peptidyl-serine phosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / skeletal muscle tissue development / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / sarcolemma / protein localization / structural constituent of cytoskeleton / Z disc / positive regulation of neuron projection development / actin binding / postsynaptic membrane / protein-containing complex assembly / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Calponin homology (CH) domain / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMuthu, M. / Richardson, K.A. / Sutherland-smith, A.J.
CitationJournal: Plos One / Year: 2012
Title: The crystal structures of dystrophin and utrophin spectrin repeats: implications for domain boundaries
Authors: Muthu, M. / Richardson, K.A. / Sutherland-Smith, A.J.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dystrophin
B: Dystrophin


Theoretical massNumber of molelcules
Total (without water)27,2842
Polymers27,2842
Non-polymers00
Water61334
1
A: Dystrophin


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dystrophin


Theoretical massNumber of molelcules
Total (without water)13,6421
Polymers13,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.040, 76.040, 66.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-7-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A356 - 370
2114B356 - 370
1214A406 - 445
2214B406 - 445

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999179, 0.032745, 0.023848), (0.030632, 0.995983, -0.084135), (-0.026508, -0.083335, -0.996169)-75.05441, 2.51944, 21.40236

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Components

#1: Protein Dystrophin /


Mass: 13642.204 Da / Num. of mol.: 2 / Fragment: Spectrin Repeat, UNP residues 338-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMD / Plasmid: pPRoExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11532
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2010 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.925
11-h,-k,l20.075
ReflectionResolution: 2.3→33.24 Å / Num. all: 9999 / Num. obs: 9035 / % possible obs: 99.9 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 7.3 % / Biso Wilson estimate: 38.01 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.7
Reflection shellHighest resolution: 2.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 11.7 / Num. unique all: 9999 / Rsym value: 0.605 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.582 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 442 4.7 %RANDOM
Rwork0.18982 ---
obs0.19327 9035 92.91 %-
all-9999 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.399 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2--2.61 Å20 Å2
3----5.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 34 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211847
X-RAY DIFFRACTIONr_bond_other_d0.0010.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9542496
X-RAY DIFFRACTIONr_angle_other_deg0.92132952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44526.2596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63815351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.282159
X-RAY DIFFRACTIONr_chiral_restr0.090.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 663 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.710.5
MEDIUM THERMAL4.115
LS refinement shellHighest resolution: 2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 9035 -
Rwork0.148 622 -
obs-9999 99.9 %
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)
110.77893.83789.08513.08664.05049.305-0.19590.27560.2569-0.3338-0.01170.1515-0.54890.05780.20760.1560.06230.00320.1033-0.04530.2368-50.537313.285910.3705
21.39930.16092.38841.6292.05166.1276-0.0332-0.03680.07930.054-0.02520.01340.0716-0.12630.05840.12240.00410.00150.1452-0.04970.2319-48.69417.381819.0399
33.2568-0.55873.9930.84270.00977.55340.0439-0.08510.15110.01010.0079-0.00360.1843-0.219-0.05180.15290.0262-0.00660.1075-0.01710.2136-42.635.56414.2787
42.1551-0.23023.74541.8507-0.70587.7905-0.0038-0.07480.19890.2714-0.0362-0.0564-0.34490.04990.040.2024-0.07080.04250.14320.00160.2761-24.633713.251110.5376
54.3436-1.71925.61811.8618-3.539712.09490.01770.27590.3412-0.2093-0.2849-0.36030.18490.45030.26720.13260.00010.01140.0910.02730.2232-26.48855.81622.2568
64.4051-0.79494.27280.4102-0.48247.89770.0201-0.22020.1572-0.0299-0.0019-0.0151-0.1325-0.3035-0.01820.1388-0.00630.02550.09730.04020.1823-32.40814.25928.7805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A338 - 367
2X-RAY DIFFRACTION2A368 - 412
3X-RAY DIFFRACTION3A413 - 453
4X-RAY DIFFRACTION4B339 - 367
5X-RAY DIFFRACTION5B368 - 412
6X-RAY DIFFRACTION6B413 - 452

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