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- PDB-5zh6: Crystal structure of Parvalbumin SPV-II of Mustelus griseus -

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Basic information

Entry
Database: PDB / ID: 5zh6
TitleCrystal structure of Parvalbumin SPV-II of Mustelus griseus
ComponentsParvalbumin SPV-II
KeywordsALLERGEN / food allergen / sea food allergy / Parvalbumin
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Parvalbumin / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...Parvalbumin / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMustelus griseus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsYang, R.Q. / Chen, Y.L. / Jin, T.C. / Cao, M.J.
CitationJournal: J. Agric. Food Chem. / Year: 2018
Title: Purification, Characterization, and Crystal Structure of Parvalbumins, the Major Allergens in Mustelus griseus.
Authors: Yang, R.Q. / Chen, Y.L. / Chen, F. / Wang, H. / Zhang, Q. / Liu, G.M. / Jin, T. / Cao, M.J.
History
DepositionMar 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Nov 22, 2023Group: 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_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parvalbumin SPV-II
B: Parvalbumin SPV-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,57810
Polymers23,0342
Non-polymers5458
Water4,089227
1
A: Parvalbumin SPV-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8856
Polymers11,5171
Non-polymers3685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Parvalbumin SPV-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6934
Polymers11,5171
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.870, 41.800, 60.340
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Parvalbumin SPV-II


Mass: 11516.769 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mustelus griseus (fish) / References: UniProt: A0A3F2YLV2*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.3 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3 M Ammonium Sulfate, 5% Ethylene Glycol, 0.1 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 30489 / % possible obs: 97.5 % / Redundancy: 5.5 % / Rrim(I) all: 0.086 / Net I/σ(I): 16.22
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6.33 / Num. unique obs: 1776 / Rrim(I) all: 0.201 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZGM
Resolution: 1.54→33.615 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2125 1558 5.11 %
Rwork0.1943 --
obs0.1953 30468 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→33.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 24 228 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141650
X-RAY DIFFRACTIONf_angle_d1.2282227
X-RAY DIFFRACTIONf_dihedral_angle_d6.567972
X-RAY DIFFRACTIONf_chiral_restr0.077259
X-RAY DIFFRACTIONf_plane_restr0.008290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5402-1.58990.2531090.20412184X-RAY DIFFRACTION81
1.5899-1.64680.24181480.19212647X-RAY DIFFRACTION100
1.6468-1.71270.25891450.19772662X-RAY DIFFRACTION99
1.7127-1.79060.24771600.20152639X-RAY DIFFRACTION99
1.7906-1.8850.22221350.19162682X-RAY DIFFRACTION100
1.885-2.00310.21400.18282656X-RAY DIFFRACTION100
2.0031-2.15780.20081240.18322689X-RAY DIFFRACTION99
2.1578-2.37490.1861760.18282652X-RAY DIFFRACTION100
2.3749-2.71840.24351450.20642671X-RAY DIFFRACTION99
2.7184-3.42430.19751350.20142706X-RAY DIFFRACTION99
3.4243-33.62260.19751410.19442722X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -1.045 Å / Origin y: -15.1621 Å / Origin z: -16.336 Å
111213212223313233
T0.0892 Å20.0022 Å2-0.0006 Å2-0.1024 Å20.0117 Å2--0.1 Å2
L0.1219 °20.2135 °20.0944 °2-0.6363 °20.4436 °2--0.3507 °2
S-0.0098 Å °0.001 Å °-0.0011 Å °-0.0316 Å °0.0251 Å °-0.0384 Å °0.0024 Å °0.0154 Å °-0.0181 Å °
Refinement TLS groupSelection details: all

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