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- PDB-3uum: Crystal Structure of N-terminal first spectrin repeat of utrophin -

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Basic information

Entry
Database: PDB / ID: 3uum
TitleCrystal Structure of N-terminal first spectrin repeat of utrophin
Componentsutrophin
KeywordsSTRUCTURAL PROTEIN / triple helical / Structural stability / cytoskeletal
Function / homology
Function and homology information


plasma membrane bounded cell projection / actin binding / postsynaptic membrane / cytoskeleton / zinc ion binding / cytoplasm
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/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
Rattus norvegicus utrophin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: utrophin
B: utrophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5823
Polymers28,5572
Non-polymers241
Water91951
1
A: utrophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3032
Polymers14,2791
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: utrophin


Theoretical massNumber of molelcules
Total (without water)14,2791
Polymers14,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.740, 58.0199, 91.2799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA312 - 3345 - 27
21ASPASPGLUGLUBB312 - 3345 - 27
12VALVALLEULEUAA342 - 43035 - 123
22VALVALLEULEUBB342 - 43035 - 123

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.988802, -0.148351, -0.016192), (-0.14823, 0.988917, -0.008415), (0.017261, -0.005921, -0.999834)20.33609, 1.34866, -55.73369

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Components

#1: Protein utrophin


Mass: 14278.683 Da / Num. of mol.: 2
Fragment: N-terminal first spectrin repeat, residues 308-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Utrn / Plasmid: pPRoExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O55147
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8000, 0.1M Na Cacodylate, 0.2M Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, SITTING 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: Jul 11, 2011 / 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
ReflectionResolution: 2→35.87 Å / Num. all: 15608 / Num. obs: 14759 / % possible obs: 98.4 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 5.7 % / Biso Wilson estimate: 34.83 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.72 / Net I/σ(I): 7.6
Reflection shellHighest resolution: 2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 7.6 / Num. unique all: 15608 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.176 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26811 774 5 %RANDOM
Rwork0.19733 ---
obs0.20066 14759 97.52 %-
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: 33.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--3.22 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 1 51 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212014
X-RAY DIFFRACTIONr_bond_other_d0.0040.021304
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9482721
X-RAY DIFFRACTIONr_angle_other_deg1.02133218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68726.923117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.277158
X-RAY DIFFRACTIONr_chiral_restr0.10.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
667MEDIUM POSITIONAL0.260.5
833LOOSE POSITIONAL0.635
667MEDIUM THERMAL3.972
833LOOSE THERMAL4.3710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 49 -
Rwork0.292 966 -
obs--96.39 %
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)
10.16660.23740.66360.36470.80074.0643-0.0085-0.02690.0532-0.0499-0.04720.06770.14880.08720.05560.06350.0084-0.00620.0528-0.02330.127220.8548-4.3201-35.5972
20.4892-0.23070.88640.1459-0.54594.5353-0.02240.08680.00480.0587-0.0281-0.00390.13960.08190.05060.10850.0002-0.00880.0183-0.00230.12960.8605-5.8059-19.668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B308 - 430
2X-RAY DIFFRACTION2A309 - 430

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