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- PDB-4edm: Crystal structure of beta-parvin CH2 domain -

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Basic information

Entry
Database: PDB / ID: 4edm
TitleCrystal structure of beta-parvin CH2 domain
ComponentsBeta-parvin
KeywordsSIGNALING PROTEIN / calponin homology domain / protein-protein interaction / LD motif / integrin signaling / focal adhesion / Adaptor protein / Paxillin / Integrin linked kinase
Function / homology
Function and homology information


establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / establishment or maintenance of cell polarity / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / lamellipodium ...establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / establishment or maintenance of cell polarity / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / focal adhesion / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for paxillin binding and focal adhesion targeting of beta-parvin.
Authors: Stiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Beta-parvin
B: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1789
Polymers30,7432
Non-polymers4347
Water2,090116
1
A: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6205
Polymers15,3721
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5584
Polymers15,3721
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.360, 67.438, 105.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-parvin / Affixin


Mass: 15371.638 Da / Num. of mol.: 2 / Fragment: C-terminal calponin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVB, CGI-56 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HBI1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 12% PEG 550 MME, 0.1M Tris, pH 7.5, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2010 / Details: mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23924 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.082 / Net I/σ(I): 25.891
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.905 / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
Blu-Ice/ DCSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.627 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1228 5.1 %RANDOM
Rwork0.2122 ---
all0.2142 23924 --
obs0.2142 23924 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.56 Å2 / Biso mean: 58.1985 Å2 / Biso min: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å20 Å2
2---3.55 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 28 116 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022189
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9862949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32124.712104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.293157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211618
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 71 -
Rwork0.344 1420 -
all-1491 -
obs-1491 89.6 %
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)
12.2801-4.5769-7.493618.279110.140327.49850.1084-0.56450.5393-0.0421.1328-1.5705-0.56381.8325-1.24120.347-0.1971-0.09630.5609-0.08220.498528.7537.7583.959
21.7093-0.37530.8367.09940.81624.1332-0.08020.1203-0.01560.29830.0901-0.21730.01260.2197-0.00990.02-0.00920.01850.1837-0.04730.148326.04522.6320.073
36.974-4.87461.84615.0715-4.628910.3709-0.309-0.0683-1.34740.73950.14481.4246-0.2617-1.05460.16420.5076-0.21250.57410.4769-0.3641.117612.38321.90926.433
43.1653-0.24572.69314.32831.445212.5464-0.2965-0.20240.2630.58740.03470.5285-0.8933-0.20040.26190.18250.02590.03980.1544-0.07980.239719.61328.58223.237
513.717-3.8337-5.19464.7881.502815.0274-0.2095-0.40260.04190.51640.1240.6012-0.6029-1.27960.08560.65330.072-0.08060.4548-0.0970.47598.7939.00820.744
62.88620.04423.18036.60453.45326.0247-0.2625-0.0890.0643-0.2908-0.09160.5391-0.8439-0.11140.35410.2878-0.0456-0.10980.2116-0.01990.276111.88729.357-6.655
74.04061.73252.1458.40442.52099.6735-0.10240.2455-0.398-0.57350.1469-0.3704-0.06260.7771-0.04450.0793-0.00770.01930.4042-0.06050.301321.97420.625-13.325
84.14440.25230.75232.85152.47097.8497-0.0928-0.01440.0825-0.3031-0.0667-0.0488-0.77180.60780.15940.189-0.1041-0.09990.28-0.0010.177820.47530.883-4.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 250
2X-RAY DIFFRACTION2A251 - 326
3X-RAY DIFFRACTION3A327 - 337
4X-RAY DIFFRACTION4A338 - 364
5X-RAY DIFFRACTION5B235 - 252
6X-RAY DIFFRACTION6B253 - 295
7X-RAY DIFFRACTION7B296 - 339
8X-RAY DIFFRACTION8B340 - 364

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