PDB-9bb8: Crystal structure of human alpha parvalbumin

ID or keywords:

Entry

Database: PDB / ID: 9bb8

Title

Crystal structure of human alpha parvalbumin

Components

Parvalbumin alpha

Keywords

METAL 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 / calcium ion binding / synapse / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.722 Å

Authors

O'Malley, A. / Chruszcz, M.

Funding support

1items

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.

History

Deposition	Apr 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2025	Group: Database references / Category: citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bb8.cif.gz	71.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9bb8.ent.gz	40.1 KB	Display	PDB format
PDBx/mmJSON format	9bb8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9bb8_validation.pdf.gz	423.2 KB	Display	wwPDB validaton report
Full document	9bb8_full_validation.pdf.gz	423.2 KB	Display
Data in XML	9bb8_validation.xml.gz	6.9 KB	Display
Data in CIF	9bb8_validation.cif.gz	8.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/9bb8 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/9bb8	HTTPS FTP

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Related structure data

Related structure data	9b26C 9barC 9bcfC 1rtpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1)

Deposited unit

A: Parvalbumin alpha

hetero molecules

13.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	96
Space group name H-M	P4₃2₁2

#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 interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.72→37.169 Å / Num. obs: 3079 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC_1/2: 0.991 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.055 / R_rim(I) all: 0.112 / R_sym value: 0.096 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.72→2.77 Å / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / Num. unique obs: 157 / CC_1/2: 0.767 / R_pim(I) all: 0.264 / R_rim(I) all: 0.546 / R_sym value: 0.471 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1RTP

1rtp

Resolution: 2.722→37.169 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2551	145	4.723 %
R_work	0.2054	2925	-
all	0.208	-	-
obs	-	3070	95.639 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 42.844 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.452 Å²	-0 Å²	-0 Å²
2-	-	-0.452 Å²	-0 Å²
3-	-	-	0.904 Å²

Refinement step

Cycle: LAST / Resolution: 2.722→37.169 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	831	0	2	18	851

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	842
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	801
X-RAY DIFFRACTION	r_angle_refined_deg	1.375	1.828	1122
X-RAY DIFFRACTION	r_angle_other_deg	0.491	1.807	1866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.177	5	109
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.564	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.852	10	162
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	10.777	10	36
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	123
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	950
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	166
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	208
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.221	0.2	725
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	436
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	430
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	28
X-RAY DIFFRACTION	r_metal_ion_refined	0.29	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.103	0.2	1
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	13
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.299	3.042	439
X-RAY DIFFRACTION	r_mcbond_other	1.297	3.042	439
X-RAY DIFFRACTION	r_mcangle_it	2.105	5.472	547
X-RAY DIFFRACTION	r_mcangle_other	2.104	5.471	548
X-RAY DIFFRACTION	r_scbond_it	1.77	3.213	403
X-RAY DIFFRACTION	r_scbond_other	1.768	3.214	404
X-RAY DIFFRACTION	r_scangle_it	2.985	5.87	575
X-RAY DIFFRACTION	r_scangle_other	2.982	5.869	576
X-RAY DIFFRACTION	r_lrange_it	5.237	36.504	3643
X-RAY DIFFRACTION	r_lrange_other	5.227	36.491	3639

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.722-2.793	0.376	10	0.282	209	0.287	227	0.889	0.941	96.4758	0.25
2.793-2.869	0.243	12	0.265	216	0.264	229	0.94	0.951	99.5633	0.238
2.869-2.951	0.265	9	0.244	201	0.245	210	0.917	0.953	100	0.216
2.951-3.042	0.256	13	0.239	193	0.241	208	0.966	0.962	99.0385	0.209
3.042-3.141	0.431	10	0.263	189	0.27	209	0.865	0.948	95.2153	0.236
3.141-3.25	0.334	11	0.24	176	0.245	198	0.932	0.964	94.4444	0.215
3.25-3.372	0.258	6	0.222	180	0.223	191	0.953	0.969	97.3822	0.201
3.372-3.508	0.381	5	0.208	180	0.214	188	0.882	0.975	98.4043	0.196
3.508-3.663	0.4	6	0.195	164	0.202	174	0.854	0.975	97.7011	0.189
3.663-3.84	0.318	8	0.187	165	0.194	176	0.964	0.978	98.2955	0.158
3.84-4.045	0.296	7	0.183	154	0.188	165	0.937	0.979	97.5758	0.168
4.045-4.287	0.232	10	0.172	139	0.176	156	0.966	0.983	95.5128	0.155
4.287-4.579	0.089	5	0.18	128	0.175	148	0.998	0.981	89.8649	0.162
4.579-4.939	0.099	8	0.142	122	0.139	141	0.991	0.986	92.1986	0.135
4.939-5.401	0.243	10	0.205	112	0.209	128	0.97	0.968	95.3125	0.18
5.401-6.023	1.285	4	0.222	111	0.241	123	0.786	0.969	93.4959	0.198
6.023-6.924	0.328	3	0.189	92	0.194	109	0.994	0.978	87.156	0.174
6.924-8.408	0.043	2	0.191	83	0.188	95	0.999	0.979	89.4737	0.196
8.408-11.598	0.09	4	0.163	65	0.157	79	0.992	0.984	87.3418	0.175
11.598-37.169	0.13	2	0.218	46	0.214	54	0.993	0.978	88.8889	0.229

Refinement TLS params.

Method: refined / Origin x: 3.958 Å / Origin y: 21.781 Å / Origin z: 5.02 Å

	11	12	13	21	22	23	31	32	33
T	0.0596 Å²	0.058 Å²	0.0032 Å²	-	0.111 Å²	0.0073 Å²	-	-	0.0179 Å²
L	2.7791 °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 group

Selection: ALL

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