PDB-3bvo: Crystal structure of human co-chaperone protein HscB

ID or keywords:

Entry

Database: PDB / ID: 3bvo

Title

Crystal structure of human co-chaperone protein HscB

Components

Co-chaperone protein HscB, mitochondrial precursor

Keywords

CHAPERONE /

Co-chaperone protein HscB / Structural Genomics Medical Relevance /

Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG /

Mitochondrion / Transit peptide

Function / homology

Function and homology information

protein maturation by iron-sulfur cluster transfer / Mitochondrial iron-sulfur cluster biogenesis /

Mitochondrial protein import / [2Fe-2S] cluster assembly /

iron-sulfur cluster assembly / ATPase activator activity / protein complex oligomerization / protein-folding chaperone binding /

mitochondrion /

nucleoplasm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Bitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain.
Authors: Bitto, E. / Bingman, C.A. / Bittova, L. / Kondrashov, D.A. / Bannen, R.M. / Fox, B.G. / Markley, J.L. / Phillips, G.N.

History

Deposition	Jan 7, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bvo.cif.gz	87.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3bvo.ent.gz	70.6 KB	Display	PDB format
PDBx/mmJSON format	3bvo.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/bv/3bvo ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvo	HTTPS FTP

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Related structure data

Similar structure data	5vh5-d 3as5-1 4xzf-1 3l0r-d 3v7m-d 2ql1-d 4bm7-1 6jij-1 4mdr-d 4hag-d 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
Other databases	TargetDB: GO.91296

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #47 - Nov 2003 Simian Virus 40 similarity (2) #80 - Aug 2006 AAA+ Proteases similarity (2)

Deposited unit

A: Co-chaperone protein HscB, mitochondrial precursor

B: Co-chaperone protein HscB, mitochondrial precursor

hetero molecules

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

1

A: Co-chaperone protein HscB, mitochondrial precursor

hetero molecules

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

2

B: Co-chaperone protein HscB, mitochondrial precursor

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.644, 32.581, 114.362
Angle α, β, γ (deg.)	90.000, 105.240, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	LYS	A	A	40 - 143	12 - 115
2	1	ARG	LYS	B	B	40 - 143	12 - 115
1	2	MSE	LEU	A	A	157 - 235	129 - 207
2	2	MSE	PRO	B	B	157 - 234	129 - 206

NCS ensembles :

ID
1
2

#1: Protein	Co-chaperone protein HscB, mitochondrial precursor / / Hsc20 / DnaJ homolog subfamily C member 20 Mass: 24397.809 Da / Num. of mol.: 2 / Fragment: Residues 30-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSCB, DNAJC20, HSC20 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8IWL3
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (16% PEG 3350, ...Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (16% PEG 3350, 0.050 M Lithium sulfate, 0.10 M PIPES pH 6.5), cryoprotected with 20% PEG 3350, 0.050 M Lithium sulfate, 0.10 M PIPES pH 6.5 in four steps up to 20% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.34 Å³/Da / Density % sol: 47.54 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (16% PEG 3350, ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97934 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2007 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 3→47.75 Å / Num. obs: 9770 / % possible obs: 96.7 % / Redundancy: 6.3 % / R_merge(I) obs: 0.086 / Χ²: 1.31 / Net I/σ(I): 10.054

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
3-3.11	4.3	0.342	3.022	780	1.071	79.8
3.11-3.23	5.1	0.287		907	1.075	90.8
3.23-3.38	5.7	0.225		952	0.999	96
3.38-3.56	6.4	0.176		990	1.095	99.9
3.56-3.78	6.7	0.123		1005	0.997	100
3.78-4.07	6.9	0.095		1010	0.857	100
4.07-4.48	7	0.079		988	1.008	100
4.48-5.13	7	0.077		1017	1.212	100
5.13-6.46	6.9	0.084		1045	1.689	100
6.46-47.75	6.7	0.058		1076	2.707	99.6

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Phasing

Phasing

Method:

SAD

Phasing MAD set

R cullis centric: 0 / Highest resolution: 3 Å / Lowest resolution: 36.78 Å / Power centric: 0

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	8021	1221
ANO_1	0.736	1.367	7824	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	12.64-36.78	0	0	88	63
ISO_1	9.22-12.64	0	0	157	58
ISO_1	7.6-9.22	0	0	203	64
ISO_1	6.62-7.6	0	0	246	63
ISO_1	5.94-6.62	0	0	294	58
ISO_1	5.44-5.94	0	0	306	59
ISO_1	5.04-5.44	0	0	364	61
ISO_1	4.72-5.04	0	0	358	65
ISO_1	4.45-4.72	0	0	421	58
ISO_1	4.23-4.45	0	0	425	62
ISO_1	4.03-4.23	0	0	445	59
ISO_1	3.86-4.03	0	0	482	62
ISO_1	3.71-3.86	0	0	488	60
ISO_1	3.58-3.71	0	0	506	59
ISO_1	3.46-3.58	0	0	557	68
ISO_1	3.35-3.46	0	0	529	52
ISO_1	3.25-3.35	0	0	552	65
ISO_1	3.16-3.25	0	0	554	63
ISO_1	3.08-3.16	0	0	544	62
ISO_1	3-3.08	0	0	502	60
ANO_1	12.64-36.78	0.316	4.425	88	0
ANO_1	9.22-12.64	0.429	3.144	157	0
ANO_1	7.6-9.22	0.419	3.309	203	0
ANO_1	6.62-7.6	0.375	3.722	246	0
ANO_1	5.94-6.62	0.414	3.212	294	0
ANO_1	5.44-5.94	0.5	2.573	306	0
ANO_1	5.04-5.44	0.58	2.144	364	0
ANO_1	4.72-5.04	0.612	1.739	358	0
ANO_1	4.45-4.72	0.716	1.418	421	0
ANO_1	4.23-4.45	0.771	1.192	425	0
ANO_1	4.03-4.23	0.8	1.062	445	0
ANO_1	3.86-4.03	0.878	0.924	482	0
ANO_1	3.71-3.86	0.925	0.694	487	0
ANO_1	3.58-3.71	0.929	0.601	502	0
ANO_1	3.46-3.58	0.945	0.486	554	0
ANO_1	3.35-3.46	0.968	0.421	527	0
ANO_1	3.25-3.35	0.976	0.333	538	0
ANO_1	3.16-3.25	0.984	0.274	515	0
ANO_1	3.08-3.16	0.987	0.239	489	0
ANO_1	3-3.08	0.992	0.198	423	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	12.806	0.456	5.7	SE	103.93	1.13
2	-5.679	0.705	98.919	SE	81.62	0.67
3	1.221	10.327	42.995	SE	120.4	0.82
4	-18.896	5.314	66.888	SE	107.71	0.75
5	3.296	11.539	72.969	SE	115.38	0.51
6	0.003	14.958	62.381	SE	138.98	0.73
7	-6.59	8.4	81.425	SE	143.49	0.67
8	22.804	15.221	87.647	SE	112.09	0.49
9	-4.035	5.94	77.516	SE	164.14	0.84

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 9241

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.19-100	74	0.56	508
6.44-8.19	71.4	0.776	504
5.63-6.44	62.6	0.801	504
5.09-5.63	68.8	0.833	505
4.71-5.09	69.3	0.871	504
4.43-4.71	59.8	0.894	503
4.2-4.43	65.3	0.877	508
4.01-4.2	71.5	0.881	503
3.86-4.01	73.6	0.87	508
3.72-3.86	74	0.842	514
3.59-3.72	76.6	0.827	503
3.49-3.59	76.7	0.812	505
3.4-3.49	77	0.796	504
3.31-3.4	82.9	0.771	505
3.23-3.31	84.9	0.76	502
3.16-3.23	84.7	0.702	504
3.09-3.16	82.7	0.664	513
3-3.09	81.8	0.651	644

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
HKL-2000		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3→47.75 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.887 / WR_factor R_free: 0.288 / WR_factor R_work: 0.236 / SU B: 47.569 / SU ML: 0.417 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.288	753	8.148 %	RANDOM
R_work	0.236	-	-	-
obs	0.24	9242	97.489 %	-

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: 72.562 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.085 Å²	0 Å²	-0.703 Å²
2-	-	4.31 Å²	0 Å²
3-	-	-	-4.765 Å²

Refinement step

Cycle: LAST / Resolution: 3→47.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3096	0	7	0	3103

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3168
X-RAY DIFFRACTION	r_angle_refined_deg	1.047	1.969	4247
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.06	5	370
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.164	24.294	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.365	15	609
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.232	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	444
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2398
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	1436
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	2162
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	105
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.265	0.2	69
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.116	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.819	2	1933
X-RAY DIFFRACTION	r_mcangle_it	1.686	6	3023
X-RAY DIFFRACTION	r_scbond_it	3.778	8	1376
X-RAY DIFFRACTION	r_scangle_it	5.666	12	1224

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	815	MEDIUM POSITIONAL	0.19	0.15
1	815	MEDIUM THERMAL	0.53	2
2	642	MEDIUM POSITIONAL	0.17	0.15
2	642	MEDIUM THERMAL	0.69	2

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	Num. reflection all	% reflection obs (%)
3-3.078	0.386	38	0.264	526	676	83.432
3.078-3.162	0.344	61	0.278	551	673	90.936
3.162-3.254	0.303	48	0.266	570	667	92.654
3.254-3.354	0.352	47	0.273	573	628	98.726
3.354-3.464	0.311	54	0.223	537	591	100
3.464-3.585	0.295	55	0.261	569	624	100
3.585-3.72	0.343	48	0.254	520	568	100
3.72-3.872	0.346	43	0.242	505	548	100
3.872-4.044	0.291	54	0.239	495	550	99.818
4.044-4.241	0.255	37	0.248	477	514	100
4.241-4.47	0.227	28	0.219	456	484	100
4.47-4.741	0.271	24	0.198	446	470	100
4.741-5.068	0.285	38	0.222	384	423	99.764
5.068-5.473	0.327	30	0.238	395	425	100
5.473-5.994	0.332	32	0.25	339	371	100
5.994-6.698	0.346	25	0.306	322	348	99.713
6.698-7.73	0.242	29	0.232	282	311	100
7.73-9.456	0.201	25	0.189	235	260	100
9.456-13.324	0.226	24	0.16	193	217	100
13.324-47.75	0.318	13	0.29	114	132	96.212

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	4.504	-0.6952	-6.6424	12.8808	-2.3843	10.7063	0.5008	1.5279	0.3766	0.1032	-0.1394	1.6538	-0.6517	-1.72	-0.3613	-0.2627	-0.1951	0.013	-0.0274	0.0731	0.0568	-8.6465	-4.8418	-19.9071
2	7.8843	2.3251	-4.99	0.8536	-1.1934	6.3723	-0.5558	0.2081	-0.8546	-0.3697	0.0078	-0.4438	0.2453	0.525	0.548	-0.3501	0.0066	0.0077	-0.4381	0.024	-0.2307	-10.9251	-13.2464	-5.4179
3	0.0111	-0.0591	-0.2643	0.3145	1.4075	6.3	-0.2702	1.7714	0.1325	3.8967	-1.2215	-0.9052	-6.2447	-0.3597	1.4917	2.2397	-0.1236	-0.2739	0.7326	0.293	0.6871	-23.1479	-2.9219	18.5916
4	8.2298	-2.1954	6.3029	2.0253	-2.6	10.1935	-0.0805	-1.0987	-0.4662	0.4562	0.1533	-0.0079	0.5185	-0.1613	-0.0728	-0.1817	0.0407	-0.0199	-0.2946	0.0527	-0.2709	-22.658	-17.7765	19.8094
5	7.8094	1.4993	-5.8376	10.3336	0.4604	39.9019	-0.5639	1.4757	-0.9399	-0.3146	-0.2942	0.6164	1.2553	-1.9555	0.8581	-0.1604	-0.3808	0.183	0.1919	-0.2674	0.0152	-10.0337	-15.0264	-29.0218
6	5.9797	2.6316	-7.2948	3.9773	-0.3075	11.888	-0.3375	1.7316	-0.6441	0.182	-0.8173	-0.4674	0.7346	-2.3392	1.1549	-0.2321	-0.2205	0.0949	0.9358	-0.3829	-0.1813	-1.3294	-9.8734	-42.1409
7	15.5769	-7.076	-1.0979	7.9651	3.2415	13.9084	-0.3186	-1.2302	-0.2524	-0.4683	0.2925	0.1264	-0.7809	-2.0973	0.0261	0.2557	-0.0139	0.0362	0.4927	0.0255	-0.2528	5.8178	-4.3285	-67.4017

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	39 - 70	11 - 42
2	X-RAY DIFFRACTION	2	A	A	71 - 147	43 - 119
3	X-RAY DIFFRACTION	3	A	A	148 - 158	120 - 130
4	X-RAY DIFFRACTION	4	A	A	159 - 235	131 - 207
5	X-RAY DIFFRACTION	5	B	B	40 - 70	12 - 42
6	X-RAY DIFFRACTION	6	B	B	71 - 143	43 - 115
7	X-RAY DIFFRACTION	7	B	B	158 - 234	130 - 206

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi