PDB-8x87: The Crystal Structure of HspBP1 from Biortus.

ID or keywords:

Entry

Database: PDB / ID: 8x87

Title

The Crystal Structure of HspBP1 from Biortus.

Components

Hsp70-binding protein 1

Keywords

CHAPERONE / Phosphoprotein

Function / homology

Function and homology information

adenyl-nucleotide exchange factor activity / molecular sequestering activity / enzyme inhibitor activity / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / ubiquitin protein ligase binding / endoplasmic reticulum / extracellular space
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: The Crystal Structure of HspBP1 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.

History

Deposition	Nov 27, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8x87.cif.gz	230.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8x87.ent.gz	178.4 KB	Display	PDB format
PDBx/mmJSON format	8x87.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x87_validation.pdf.gz	449.9 KB	Display	wwPDB validaton report
Full document	8x87_full_validation.pdf.gz	455.2 KB	Display
Data in XML	8x87_validation.xml.gz	42 KB	Display
Data in CIF	8x87_validation.cif.gz	61.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/8x87 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/8x87	HTTPS FTP

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Related structure data

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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Hsp70-binding protein 1

B: Hsp70-binding protein 1

C: Hsp70-binding protein 1

D: Hsp70-binding protein 1

124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hsp70-binding protein 1

defined by author
Evidence: gel filtration
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hsp70-binding protein 1

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

3

C: Hsp70-binding protein 1

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

4

D: Hsp70-binding protein 1

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

Unit cell

Length a, b, c (Å)	76.931, 89.411, 84.680
Angle α, β, γ (deg.)	90.000, 90.000, 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	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 87 - 350 / Label seq-ID: 4 - 267

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Hsp70-binding protein 1 Mass: 30888.574 Da / Num. of mol.: 4 / Mutation: E88G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZL4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.36 Å³/Da / Density % sol: 47.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18053 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.18053 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.03 Å / Num. obs: 56950 / % possible obs: 97.8 % / Redundancy: 3.5 % / R_merge(I) obs: 0.082 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.2→2.26 Å / R_merge(I) obs: 0.627 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4332 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→48 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.948 / SU B: 8.528 / SU ML: 0.198 / Cross valid method: FREE R-VALUE / ESU R: 0.31 / ESU R Free: 0.227
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2491	2854	5.013 %
R_work	0.1992	54075	-
all	0.202	-	-
obs	-	56929	97.625 %

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: 34.488 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.76 Å²	-0 Å²	0.038 Å²
2-	-	-2.439 Å²	0 Å²
3-	-	-	-1.321 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8240	0	0	604	8844

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	8366
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7808
X-RAY DIFFRACTION	r_angle_refined_deg	1.381	1.638	11266
X-RAY DIFFRACTION	r_angle_other_deg	0.466	1.554	18224
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.295	5	1056
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.03	5	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.358	10	1570
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.985	10	410
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1282
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9644
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1548
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1978
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	7012
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	4085
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	4658
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	407
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.057	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.178	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.164	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.194	0.2	42
X-RAY DIFFRACTION	r_mcbond_it	3.002	3.523	4224
X-RAY DIFFRACTION	r_mcbond_other	3.001	3.523	4224
X-RAY DIFFRACTION	r_mcangle_it	4.648	5.274	5274
X-RAY DIFFRACTION	r_mcangle_other	4.648	5.274	5275
X-RAY DIFFRACTION	r_scbond_it	4.072	4.118	4142
X-RAY DIFFRACTION	r_scbond_other	4.071	4.119	4143
X-RAY DIFFRACTION	r_scangle_it	6.632	5.981	5990
X-RAY DIFFRACTION	r_scangle_other	6.631	5.982	5991
X-RAY DIFFRACTION	r_lrange_it	8.235	49.716	9609
X-RAY DIFFRACTION	r_lrange_other	8.243	47.344	9485
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.069	0.05	8561
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	8544
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.072	0.05	8565
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	8603
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.07	0.05	8569
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.073	0.05	8548

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	0.06949	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06949	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06689	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06689	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07169	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07169	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06625	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06625	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06984	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06984	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07341	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07341	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.257	0.396	209	0.313	3886	X-RAY DIFFRACTION	96.5574
2.257-2.319	0.313	217	0.3	3865	X-RAY DIFFRACTION	96.6611
2.319-2.386	0.283	192	0.27	3705	X-RAY DIFFRACTION	96.8199
2.386-2.459	0.295	175	0.26	3660	X-RAY DIFFRACTION	96.7213
2.459-2.539	0.273	167	0.236	3548	X-RAY DIFFRACTION	97.2259
2.539-2.628	0.3	161	0.234	3450	X-RAY DIFFRACTION	97.4892
2.628-2.727	0.354	183	0.228	3318	X-RAY DIFFRACTION	97.4666
2.727-2.838	0.324	190	0.22	3158	X-RAY DIFFRACTION	97.8947
2.838-2.964	0.291	187	0.212	3080	X-RAY DIFFRACTION	98.1376
2.964-3.108	0.281	146	0.193	2934	X-RAY DIFFRACTION	98.0892
3.108-3.275	0.272	119	0.193	2840	X-RAY DIFFRACTION	97.9801
3.275-3.473	0.266	136	0.188	2672	X-RAY DIFFRACTION	98.4227
3.473-3.712	0.253	143	0.186	2495	X-RAY DIFFRACTION	98.4696
3.712-4.007	0.193	95	0.168	2348	X-RAY DIFFRACTION	98.5478
4.007-4.386	0.175	141	0.136	2170	X-RAY DIFFRACTION	98.5921
4.386-4.899	0.175	115	0.147	1919	X-RAY DIFFRACTION	97.8355
4.899-5.647	0.231	101	0.163	1720	X-RAY DIFFRACTION	98.4857
5.647-6.892	0.301	71	0.185	1497	X-RAY DIFFRACTION	98.6784
6.892-9.649	0.165	60	0.142	1153	X-RAY DIFFRACTION	98.4578
9.649-48	0.154	46	0.203	657	X-RAY DIFFRACTION	97.0994

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