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- PDB-9bb8: Crystal structure of human alpha parvalbumin -

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Basic information

Entry
Database: PDB / ID: 9bb8
TitleCrystal structure of human alpha parvalbumin
ComponentsParvalbumin alpha
KeywordsMETAL BINDING PROTEIN / parvalbumin / calcium binding protein
Function / homology
Function and homology information


inhibitory chemical synaptic transmission / Transcriptional Regulation by MECP2 / excitatory chemical synaptic transmission / gene expression / axon / synapse / calcium ion binding / cytoplasm
Similarity search - Function
Parvalbumin / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.722 Å
AuthorsO'Malley, A. / Chruszcz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Protein Sci. / Year: 2024
Title: Comparative studies of seafood and reptile alpha- and beta-parvalbumins.
Authors: O'Malley, A. / Ray, J.M. / Kitlas, P. / Ruethers, T. / Kapingidza, A.B. / Cierpicki, T. / Lopata, A. / Kowal, K. / Chruszcz, M.
#1: Journal: Protein Sci. / Year: 2024
Title: Crystal structure of the alpha parvalbumin from thornback ray
Authors: O'Malley, A. / Kapingidza, A.B. / Ruethers, T. / Lopata, A.L. / Chruszcz, M.
History
DepositionApr 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parvalbumin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8963
Polymers13,8161
Non-polymers802
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.112, 83.112, 31.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Parvalbumin alpha


Mass: 13815.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVALB / Production host: Escherichia coli (E. coli) / References: UniProt: P20472
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3.4 M sodium malonate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→37.169 Å / Num. obs: 3079 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.055 / Rrim(I) all: 0.112 / Rsym value: 0.096 / Net I/σ(I): 11.6
Reflection shellResolution: 2.72→2.77 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / Num. unique obs: 157 / CC1/2: 0.767 / Rpim(I) all: 0.264 / Rrim(I) all: 0.546 / Rsym value: 0.471 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RTP

1rtp


Resolution: 2.722→37.169 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 30.62 / SU ML: 0.309 / Cross valid method: FREE R-VALUE / ESU R Free: 0.386
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2551 145 4.723 %
Rwork0.2054 2925 -
all0.208 --
obs-3070 95.639 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 42.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.452 Å2-0 Å2-0 Å2
2---0.452 Å2-0 Å2
3---0.904 Å2
Refinement stepCycle: LAST / Resolution: 2.722→37.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 2 18 851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.012842
X-RAY DIFFRACTIONr_bond_other_d0.0010.016801
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.8281122
X-RAY DIFFRACTIONr_angle_other_deg0.4911.8071866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.56451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85210162
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.7771036
X-RAY DIFFRACTIONr_chiral_restr0.0610.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02166
X-RAY DIFFRACTIONr_nbd_refined0.2150.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.2725
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2436
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.228
X-RAY DIFFRACTIONr_metal_ion_refined0.290.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.21
X-RAY DIFFRACTIONr_nbd_other0.2060.213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.23
X-RAY DIFFRACTIONr_mcbond_it1.2993.042439
X-RAY DIFFRACTIONr_mcbond_other1.2973.042439
X-RAY DIFFRACTIONr_mcangle_it2.1055.472547
X-RAY DIFFRACTIONr_mcangle_other2.1045.471548
X-RAY DIFFRACTIONr_scbond_it1.773.213403
X-RAY DIFFRACTIONr_scbond_other1.7683.214404
X-RAY DIFFRACTIONr_scangle_it2.9855.87575
X-RAY DIFFRACTIONr_scangle_other2.9825.869576
X-RAY DIFFRACTIONr_lrange_it5.23736.5043643
X-RAY DIFFRACTIONr_lrange_other5.22736.4913639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.722-2.7930.376100.2822090.2872270.8890.94196.47580.25
2.793-2.8690.243120.2652160.2642290.940.95199.56330.238
2.869-2.9510.26590.2442010.2452100.9170.9531000.216
2.951-3.0420.256130.2391930.2412080.9660.96299.03850.209
3.042-3.1410.431100.2631890.272090.8650.94895.21530.236
3.141-3.250.334110.241760.2451980.9320.96494.44440.215
3.25-3.3720.25860.2221800.2231910.9530.96997.38220.201
3.372-3.5080.38150.2081800.2141880.8820.97598.40430.196
3.508-3.6630.460.1951640.2021740.8540.97597.70110.189
3.663-3.840.31880.1871650.1941760.9640.97898.29550.158
3.84-4.0450.29670.1831540.1881650.9370.97997.57580.168
4.045-4.2870.232100.1721390.1761560.9660.98395.51280.155
4.287-4.5790.08950.181280.1751480.9980.98189.86490.162
4.579-4.9390.09980.1421220.1391410.9910.98692.19860.135
4.939-5.4010.243100.2051120.2091280.970.96895.31250.18
5.401-6.0231.28540.2221110.2411230.7860.96993.49590.198
6.023-6.9240.32830.189920.1941090.9940.97887.1560.174
6.924-8.4080.04320.191830.188950.9990.97989.47370.196
8.408-11.5980.0940.163650.157790.9920.98487.34180.175
11.598-37.1690.1320.218460.214540.9930.97888.88890.229
Refinement TLS params.Method: refined / Origin x: 3.958 Å / Origin y: 21.781 Å / Origin z: 5.02 Å
111213212223313233
T0.0596 Å20.058 Å20.0032 Å2-0.111 Å20.0073 Å2--0.0179 Å2
L2.7791 °2-0.0371 °2-1.1441 °2-3.6616 °2-0.1107 °2--3.4958 °2
S-0.0631 Å °0.124 Å °-0.084 Å °0.0638 Å °-0.0079 Å °-0.06 Å °0.1248 Å °-0.0105 Å °0.0711 Å °
Refinement TLS groupSelection: ALL

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