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- PDB-7vzo: crystal structure of Domain 5-6 of filamin C from Scylla paramamosain -

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Basic information

Entry
Database: PDB / ID: 7vzo
Titlecrystal structure of Domain 5-6 of filamin C from Scylla paramamosain
ComponentsFilamin C
KeywordsALLERGEN / Glycoprotein / myogen
Function / homology
Function and homology information


actin filament binding / actin cytoskeleton organization
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / Filamin C
Similarity search - Component
Biological speciesScylla paramamosain (green mud crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHe, X. / Jin, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Crystal Structure Analysis and IgE Epitope Mapping of Allergic Predominant Region in Scylla paramamosain Filamin C, Scy p 9.
Authors: He, X.R. / Yang, Y. / Kang, S. / Chen, Y.X. / Zheng, P.Y. / Chen, G.X. / Chen, X.M. / Cao, M.J. / Jin, T. / Liu, G.M.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Filamin C
B: Filamin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,39519
Polymers42,3452
Non-polymers1,04917
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint1 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.604, 70.723, 59.012
Angle α, β, γ (deg.)90.000, 113.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Filamin C


Mass: 21172.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scylla paramamosain (green mud crab) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5J6X3F8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2 M ammonium acetate 0.1 M HEPES pH 7.8 20%(V/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.75→24.22 Å / Num. obs: 39401 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.064 / Net I/σ(I): 8.5 / Num. measured all: 77080
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Num. unique obs: 2184 / CC1/2: 0.636 / Rpim(I) all: 0.24 / Rrim(I) all: 0.339 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.508
Highest resolutionLowest resolution
Rotation24.22 Å3 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J3S

2j3s


Resolution: 1.75→24.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.098 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1850 4.7 %RANDOM
Rwork0.1614 ---
obs0.1634 37529 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.22 Å2 / Biso mean: 18.1 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0.15 Å2
2--1.07 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.75→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 68 414 3400
Biso mean--24.71 34.46 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133041
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172861
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6664088
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5796621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19822.078154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9611520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 127 -
Rwork0.2 2767 -
all-2894 -
obs--99.93 %

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