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- PDB-3fs7: Crystal structure of Gallus gallus beta-parvalbumin (avian thymic... -

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Basic information

Entry
Database: PDB / ID: 3fs7
TitleCrystal structure of Gallus gallus beta-parvalbumin (avian thymic hormone)
ComponentsParvalbumin, thymic
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / EF-HAND / parvalbumin / Acetylation / Calcium
Function / homology
Function and homology information


calcium ion binding / cytoplasm
Similarity search - Function
Parvalbumin / EF-hand domain / 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 ...Parvalbumin / EF-hand domain / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9539 Å
AuthorsSchuermann, J.P. / Tanner, J.J. / Henzl, M.T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states.
Authors: Schuermann, J.P. / Tan, A. / Tanner, J.J. / Henzl, M.T.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.3Sep 6, 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 / struct_site
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 / _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: Parvalbumin, thymic
B: Parvalbumin, thymic
C: Parvalbumin, thymic
D: Parvalbumin, thymic
E: Parvalbumin, thymic
F: Parvalbumin, thymic
G: Parvalbumin, thymic
H: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,19931
Polymers93,8978
Non-polymers1,30223
Water8,089449
1
A: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9134
Polymers11,7371
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9134
Polymers11,7371
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9094
Polymers11,7371
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9094
Polymers11,7371
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8173
Polymers11,7371
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9094
Polymers11,7371
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9134
Polymers11,7371
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Parvalbumin, thymic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9134
Polymers11,7371
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.644, 51.560, 67.633
Angle α, β, γ (deg.)87.42, 85.42, 87.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Parvalbumin, thymic / / Avian thymic hormone / ATH / Thymus-specific antigen T1


Mass: 11737.092 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19753
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 1.76 Å3/Da / Density % sol: 30.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The reservoir contained 70% saturated ammonium sulfate, 100 micromolar calcium ion, 10 millimolar MES buffer. The volume of the hanging drop was 80 microliters. , pH 6.0, VAPOR DIFFUSION, ...Details: The reservoir contained 70% saturated ammonium sulfate, 100 micromolar calcium ion, 10 millimolar MES buffer. The volume of the hanging drop was 80 microliters. , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 / Details: MD2 micro-diffractometer with 20 micron aperature
RadiationMonochromator: single crystal side-bounce 220 silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 45451 / Num. obs: 45451 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.086 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4474 / Rsym value: 0.42 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RWY

1rwy


Resolution: 1.9539→35.632 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.27 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.09 / Stereochemistry target values: ML
Details: TLS performed using each chain as a separate TLS group
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 2288 5.04 %Random
Rwork0.1635 ---
obs0.1663 45426 97.87 %-
all-45451 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.674 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 76.47 Å2 / Biso mean: 21.218 Å2 / Biso min: 4.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.534 Å20.82 Å24.831 Å2
2---2.294 Å23.079 Å2
3----0.241 Å2
Refinement stepCycle: LAST / Resolution: 1.9539→35.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 54 449 6983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg0.715
X-RAY DIFFRACTIONf_dihedral_angle_d14.7
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9539-1.99640.28311370.20582654X-RAY DIFFRACTION95
1.9964-2.04280.22031440.18532640X-RAY DIFFRACTION97
2.0428-2.09390.25621390.17322683X-RAY DIFFRACTION97
2.0939-2.15050.25991440.17122681X-RAY DIFFRACTION97
2.1505-2.21380.24971360.16882661X-RAY DIFFRACTION97
2.2138-2.28520.22881470.16312690X-RAY DIFFRACTION98
2.2852-2.36690.25311440.1562685X-RAY DIFFRACTION98
2.3669-2.46160.24591460.17062711X-RAY DIFFRACTION98
2.4616-2.57360.21741280.1732706X-RAY DIFFRACTION98
2.5736-2.70930.26141510.16932690X-RAY DIFFRACTION98
2.7093-2.8790.23961390.17552712X-RAY DIFFRACTION98
2.879-3.10110.24761610.16862699X-RAY DIFFRACTION99
3.1011-3.4130.18851340.16032755X-RAY DIFFRACTION99
3.413-3.90630.17241400.14072705X-RAY DIFFRACTION99
3.9063-4.91950.17181560.13162724X-RAY DIFFRACTION99
4.9195-35.63760.20811420.17122742X-RAY DIFFRACTION99
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)
10.4889-0.15360.29560.05250.12520.30970.0157-0.0756-0.0576-0.0050.01920.0064-0.0148-0.0542-0.01580.05710.00260.01060.08780.01920.06986.41961.856265.6915
20.63480.4531-0.23920.09150.21190.82230.1718-0.0423-0.03310.0374-0.024-0.0622-0.0989-0.0974-0.07150.09030.00190.00630.06660.00920.079218.750831.128461.4432
30.56610.01790.10160.74570.16520.26990.0161-0.0104-0.0074-0.0573-0.00120.0092-0.0220.0249-0.0020.0578-0.00810.01840.0458-0.01320.055330.400812.843653.4697
40.45240.07010.34860.60920.26940.2703-0.02650.02010.0033-0.02310.0089-0.0915-0.02820.01090.01320.0521-0.00140.00490.02860.00080.062337.889542.563543.1775
50.4423-0.2263-0.07170.3030.18630.75050.0437-0.0125-0.0069-0.0415-0.01160.0223-0.10930.0674-0.01250.0843-0.0163-0.02040.0699-0.00990.058225.62833.010117.0598
60.4538-0.2629-0.01280.12630.79550.63860.02490.02080.01550.0324-0.0805-0.00920.039-0.07030.01810.04590.00920.00320.0461-0.00060.03656.656216.22234.8764
70.6828-0.56730.47490.4004-0.49310.63860.02550.1260.1283-0.0059-0.121-0.04320.09260.13910.05190.06980.0016-0.00550.09420.00820.072137.23924.90213.036
80.4185-0.25250.00820.346-0.01840.59750.0012-0.0817-0.10630.02170.17270.1853-0.012-0.1494-0.09120.04870.0045-0.00190.08760.06320.1114.917937.520626.0354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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