PDB-8zlc: Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum

ID or keywords:

Entry

Database: PDB / ID: 8zlc

Title

Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum

Components

Ankyrin-repeat protein

Keywords

STRUCTURAL PROTEIN / Protein-Protein interaction / Ankyrin Repeat / invasion Complex

Function / homology

Ankyrin repeats (many copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ankyrin-repeat protein, putative

Function and homology information

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Kumari, P. / Gautam, A.K. / Gourinath, S. / Malhotra, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum
Authors: Kumari, P. / Gautam, A.K. / Gourinath, S. / Malhotra, P.

History

Deposition	May 18, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zlc.cif.gz	69.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8zlc.ent.gz	48.7 KB	Display	PDB format
PDBx/mmJSON format	8zlc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zl/8zlc ftp://data.pdbj.org/pub/pdb/validation_reports/zl/8zlc	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ankyrin-repeat protein

B: Ankyrin-repeat protein

31.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	42.377, 62.742, 91.784
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 135 / Label seq-ID: 3 - 135

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Ankyrin-repeat protein Mass: 15580.159 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PF3D7_1410800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ILY7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H₂O
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: 1.96 Å³/Da / Density % sol: 37.18 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium Acetate, 25% PEG 3350, 0.1M bis-tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 2.13→51.8 Å / Num. obs: 18741 / % possible obs: 99.94 % / Redundancy: 4.82 % / CC_1/2: 0.994 / Net I/σ(I): 5.35
Reflection shell	Resolution: 2.13→2.185 Å / Num. unique obs: 910 / CC_1/2: 0.732

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.13→51.797 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.905 / SU B: 5.455 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2287	711	4.99 %
R_work	0.1847	13538	-
all	0.187	-	-
obs	-	14249	99.853 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.033 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.195 Å²	-0 Å²	0 Å²
2-	-	0.939 Å²	-0 Å²
3-	-	-	0.256 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→51.797 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2103	0	0	113	2216

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	2140
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2109
X-RAY DIFFRACTION	r_angle_refined_deg	1.539	1.63	2894
X-RAY DIFFRACTION	r_angle_other_deg	1.313	1.585	4841
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.6	5	270
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.174	24.632	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.752	15	402
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.744	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	291
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2412
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	458
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	461
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	1917
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	1095
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	976
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.101	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.2	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.145	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.143	2.647	1080
X-RAY DIFFRACTION	r_mcbond_other	2.14	2.646	1079
X-RAY DIFFRACTION	r_mcangle_it	3.209	3.957	1347
X-RAY DIFFRACTION	r_mcangle_other	3.208	3.958	1348
X-RAY DIFFRACTION	r_scbond_it	3.1	3.126	1060
X-RAY DIFFRACTION	r_scbond_other	3.099	3.126	1060
X-RAY DIFFRACTION	r_scangle_it	4.928	4.504	1546
X-RAY DIFFRACTION	r_scangle_other	4.928	4.503	1546
X-RAY DIFFRACTION	r_lrange_it	6.251	32.58	2462
X-RAY DIFFRACTION	r_lrange_other	6.244	32.513	2451
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.13	0.05	3826

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.1297	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.1297	0.05007

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
2.13-2.185	0.208	56	0.226	968	0.224	1027	0.937	0.909	99.7079	0.218
2.185-2.245	0.234	46	0.218	985	0.218	1033	0.915	0.923	99.8064	0.206
2.245-2.31	0.245	49	0.19	897	0.193	946	0.917	0.94	100	0.181
2.31-2.381	0.204	38	0.202	923	0.203	964	0.927	0.926	99.6888	0.195
2.381-2.459	0.281	46	0.201	875	0.205	922	0.902	0.925	99.8915	0.199
2.459-2.545	0.223	56	0.205	843	0.206	899	0.924	0.931	100	0.206
2.545-2.641	0.257	45	0.204	837	0.207	883	0.917	0.926	99.8867	0.207
2.641-2.748	0.301	44	0.205	766	0.21	810	0.868	0.927	100	0.211
2.748-2.87	0.228	35	0.205	771	0.206	808	0.914	0.929	99.7525	0.215
2.87-3.01	0.265	34	0.185	743	0.188	777	0.931	0.94	100	0.198
3.01-3.172	0.26	34	0.185	700	0.188	734	0.919	0.951	100	0.199
3.172-3.364	0.2	33	0.177	653	0.178	686	0.947	0.955	100	0.196
3.364-3.595	0.233	35	0.163	640	0.166	675	0.95	0.964	100	0.19
3.595-3.881	0.21	31	0.16	579	0.162	610	0.946	0.966	100	0.191
3.881-4.249	0.237	28	0.162	552	0.165	580	0.945	0.967	100	0.199
4.249-4.747	0.195	26	0.154	495	0.156	521	0.974	0.967	100	0.197
4.747-5.473	0.173	24	0.181	434	0.18	458	0.967	0.961	100	0.233
5.473-6.685	0.202	22	0.184	381	0.185	403	0.97	0.961	100	0.229
6.685-9.376	0.121	18	0.18	309	0.176	327	0.961	0.941	100	0.257
9.376-51.797	0.429	11	0.197	185	0.211	205	0.697	0.94	95.6098	0.401

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