PDB-3l4i: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HSP70 (CGD2_20) FRO...

ID or keywords:

Entry

Database: PDB / ID: 3l4i

Title

CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HSP70 (CGD2_20) FROM Cryptosporidium PARVUM IN COMPLEX WITH ADP and inorganic phosphate

Components

Heat shock 70 (HSP70) protein

Keywords

CHAPERONE / atp binding domain / heat shock protein / structural genomics / atp-binding / nucleotide binding / stress response / Structural Genomics Consortium / SGC / Nucleotide-binding

Function / homology

Function and homology information

SRP-dependent cotranslational protein targeting to membrane, translocation / ATP-dependent protein folding chaperone / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Lew, J. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. ...

Citation

Journal: To be Published
Title: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HSP70 (CGD2_20) FROM Cryptosporidium PARVUM IN COMPLEX WITH ADP and inorganic phosphate
Authors: Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Lew, J. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Hills, T.

History

Deposition	Dec 20, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 2023	Group: 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l4i.cif.gz	280.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3l4i.ent.gz	220.5 KB	Display	PDB format
PDBx/mmJSON format	3l4i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l4i_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3l4i_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3l4i_validation.xml.gz	32.8 KB	Display
Data in CIF	3l4i_validation.cif.gz	47.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4i ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4i	HTTPS FTP

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Related structure data

Related structure data	3kvgS S: Starting model for refinement
Similar structure data	6cz1-1 3iuc-3 5mkr-d 1kej-d 2qw9-2 3gl1-2 7nqt-2 6ha7-1 2qwm-2 4ar9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#32 - Aug 2002 Chaperones similarity (9)

Deposited unit

A: Heat shock 70 (HSP70) protein

B: Heat shock 70 (HSP70) protein

hetero molecules

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

1

A: Heat shock 70 (HSP70) protein

hetero molecules

defined by author&software
44.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Heat shock 70 (HSP70) protein

hetero molecules

defined by author&software
44.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.977, 115.324, 182.314
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-558- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Heat shock 70 (HSP70) protein Mass: 44229.855 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 15-396) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd2_20 / Plasmid: PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q5CPP8

#1: Protein

Heat shock 70 (HSP70) protein

Mass: 44229.855 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 15-396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd2_20 / Plasmid: PET15 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q5CPP8

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Non-polymers , 5 types, 428 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4 mM MgCl2, 2 mM TCEP,20% P3350, 0.2M KCl, 2 mM ADP, 4 mM MgCL2, 2 mM TCEP, 25% Ethylene Glycol - Cryoprotectant, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 46364 / Num. obs: 46272 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / B_iso Wilson estimate: 43 Å² / R_merge(I) obs: 0.057 / R_sym value: 0.034 / Χ²: 1.609 / Net I/σ(I): 14.7
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.824 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2291 / R_sym value: 0.748 / Χ²: 1.636 / % possible all: 100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3kvg

3kvg

Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.927 / WR_factor R_free: 0.244 / WR_factor R_work: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.83 / SU B: 14.439 / SU ML: 0.164 / SU R Cruickshank DPI: 0.176 / SU R_free: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	2336	5.1 %	RANDOM
R_work	0.206	-	-	-
all	0.209	46427	-	-
obs	0.209	46233	99.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 72.55 Å² / B_iso mean: 11.246 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0 Å²
2-	-	-0.77 Å²	0 Å²
3-	-	-	1.23 Å²

Refine analyze

Luzzati coordinate error obs: 0.379 Å

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6039	0	73	421	6533

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6226
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4239
X-RAY DIFFRACTION	r_angle_refined_deg	1.256	1.971	8459
X-RAY DIFFRACTION	r_angle_other_deg	0.819	3	10321
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.301	5	807
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.012	23.986	286
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.305	15	1067
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.438	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	944
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7113
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1283
X-RAY DIFFRACTION	r_mcbond_it	0.673	1.5	3915
X-RAY DIFFRACTION	r_mcbond_other	0.135	1.5	1603
X-RAY DIFFRACTION	r_mcangle_it	1.245	2	6311
X-RAY DIFFRACTION	r_scbond_it	1.835	3	2311
X-RAY DIFFRACTION	r_scangle_it	2.94	4.5	2147
X-RAY DIFFRACTION	r_rigid_bond_restr	0.738	3	10465

LS refinement shell

Resolution: 2.198→2.255 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	152	-
R_work	0.267	3147	-
all	-	3299	-
obs	-	-	96.72 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.9783	0.6153	0.234	0.4601	0.3976	0.6296	-0.0476	0.004	0.0464	-0.062	0.0005	0.0797	0.0639	0.0248	0.0471	0.4531	0.0162	-0.0119	0.3735	0.0082	0.4448	7.8396	3.7539	49.0099
2	0.8901	-0.7314	-0.0561	2.3811	0.1059	1.0651	-0.0257	-0.0025	0.0502	-0.131	0.0359	-0.0416	-0.1524	0.1393	-0.0103	0.4267	-0.0414	-0.0136	0.3908	0.0124	0.4476	21.7431	19.2548	50.6896
3	2.2381	-1.7816	-1.0867	4.5806	1.2541	1.7906	0.022	-0.226	0.0401	0.0672	0.075	-0.3662	-0.1639	0.4756	-0.097	0.3274	-0.0381	-0.056	0.499	0.001	0.4679	33.0163	15.6274	58.1093
4	4.8813	0.5602	0.1983	0.315	0.095	0.1599	0.0007	-0.1591	0.0392	0.0638	-0.055	0.0654	-0.0199	0.0621	0.0543	0.4562	0.0082	-0.0275	0.404	-0.0039	0.4253	11.7747	10.1645	57.8545
5	0.6479	0.0252	0.2803	0.5201	0.2462	0.3916	-0.0464	-0.1205	-0.1413	0.0737	0.0218	-0.0028	0.1213	0.0875	0.0247	0.4599	0.0414	0.0017	0.4076	0.0378	0.4365	18.4512	-2.3668	56.9226
6	0.61	-0.6298	-0.03	5.3516	-0.7181	1.1841	-0.0632	-0.0115	-0.1077	0.1194	0.1954	0.1929	0.1452	0.0777	-0.1322	0.4542	0.0846	0.0084	0.3823	0.0263	0.4409	20.7572	-12.0766	42.8594
7	2.0455	1.2862	-0.7699	7.5734	-3.5521	3.1243	-0.0274	0.223	0.367	-0.4336	-0.1322	-0.3537	0.2025	0.4552	0.1597	0.3498	0.0399	0.0099	0.4558	-0.0536	0.5654	28.4513	7.1003	34.2737
8	0.3139	-1.3172	-0.2598	5.8969	1.897	4.1764	-0.0361	0.0362	0.3049	0.0212	0.0089	-0.5948	-0.224	0.4578	0.0272	0.4027	-0.0145	-0.0062	0.4295	0.0749	0.6038	21.4979	19.1916	31.3363
9	1.0479	-0.7215	0.3951	2.4974	-0.7284	0.3261	0.0035	0.1546	0.127	-0.1557	-0.0419	-0.189	0.1713	0.1402	0.0384	0.4225	0.0386	0.0589	0.3939	0.018	0.4459	23.763	0.8177	29.2755
10	1.2075	-0.5292	0.312	0.9242	1.3629	1.6629	-0.0595	0.0723	-0.1858	0.0738	-0.0373	0.1755	0.1217	0.036	0.0967	0.4822	0.019	0.0276	0.3501	0.0139	0.4847	10.4325	-5.8394	46.3999
11	1.4388	0.2965	0.764	1.3379	0.1352	0.6277	0.0282	0.1733	-0.0632	-0.1321	-0.1076	-0.2059	0.0099	-0.0186	0.0794	0.4365	-0.0037	0.0119	0.413	0.0111	0.4005	-3.4632	16.8066	18.7457
12	4.2948	-0.1641	-0.984	6.5876	1.8956	5.0303	-0.1029	0.5132	0.2139	-0.4316	-0.0487	0.2912	-0.2746	-0.584	0.1516	0.4614	0.122	-0.1729	0.4726	0.0329	0.3149	-19.4269	28.8878	9.631
13	1.4601	-0.158	0.9623	0.9207	-0.2961	1.2659	0.0103	0.0966	-0.0215	-0.0541	-0.0967	-0.0551	-0.0725	-0.0935	0.0864	0.4317	0.001	-0.0252	0.4373	0.0002	0.3796	-11.8729	17.3591	23.8789
14	1.6336	-0.094	0.3226	0.7011	-0.1726	0.1447	-0.0927	0.031	0.1995	0.1263	-0.0689	-0.1056	-0.2084	-0.0674	0.1616	0.5244	0.0003	-0.0829	0.3509	0.0602	0.455	-3.0178	32.4928	24.5507
15	1.3807	0.2864	0.0937	3.4869	2.3072	4.9495	0.0707	0.1727	0.2718	0.0149	-0.1916	-0.5503	-0.3172	0.0839	0.1209	0.5859	-0.0714	-0.0693	0.3216	0.1637	0.465	7.3401	40.3177	16.8833
16	1.2036	0.6675	0.5139	9.0756	5.712	3.0019	-0.3243	0.6957	0.0472	-1.4434	0.2191	0.2571	-1.0032	0.1205	0.1051	0.7379	-0.1738	0.0564	0.7095	-0.0044	0.2409	-1.7263	15.0522	-6.681
17	13.01	8.227	3.9403	9.1676	6.3427	6.2014	-0.143	0.0536	-0.5761	-0.3495	0.3891	-1.0876	0.3823	-0.3974	-0.2462	0.6189	-0.2266	0.2811	0.7355	-0.2408	0.3697	3.8176	12.1219	1.8448
18	-0.4791	1.4126	2.2427	5.3878	4.8442	9.1139	-0.3333	1.0702	0.0958	-1.0827	0.6007	-0.1677	-0.2695	1.4334	-0.2675	0.5007	-0.298	0.2625	1.1268	0.0379	0.2899	7.5798	19.6114	-3.6002
19	1.8706	1.9184	0.0087	7.3228	-0.6419	3.9791	-0.3101	0.2296	-0.151	-0.3135	0.2173	-0.7254	-0.3584	0.3779	0.0927	0.4657	-0.1402	0.0928	0.4287	0.1322	0.454	13.9785	35.0122	9.714
20	3.3386	-0.4709	-4.4174	2.24	0.4093	4.1831	0.1173	-0.0672	0.2522	0.1384	-0.0008	-0.4758	-0.2852	0.122	-0.1165	0.5176	-0.0631	-0.1259	0.3645	0.0947	0.5727	6.2608	29.8433	30.7131

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 54
2	X-RAY DIFFRACTION	2	A	55 - 90
3	X-RAY DIFFRACTION	3	A	91 - 129
4	X-RAY DIFFRACTION	4	A	130 - 154
5	X-RAY DIFFRACTION	5	A	155 - 201
6	X-RAY DIFFRACTION	6	A	202 - 228
7	X-RAY DIFFRACTION	7	A	229 - 270
8	X-RAY DIFFRACTION	8	A	271 - 291
9	X-RAY DIFFRACTION	9	A	292 - 374
10	X-RAY DIFFRACTION	10	A	375 - 399
11	X-RAY DIFFRACTION	11	B	19 - 89
12	X-RAY DIFFRACTION	12	B	90 - 115
13	X-RAY DIFFRACTION	13	B	116 - 156
14	X-RAY DIFFRACTION	14	B	157 - 201
15	X-RAY DIFFRACTION	15	B	202 - 242
16	X-RAY DIFFRACTION	16	B	243 - 275
17	X-RAY DIFFRACTION	17	B	276 - 291
18	X-RAY DIFFRACTION	18	B	292 - 337
19	X-RAY DIFFRACTION	19	B	338 - 384
20	X-RAY DIFFRACTION	20	B	385 - 400

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