PDB-3br8: Crystal structure of acylphosphatase from Bacillus subtilis

ID or keywords:

Entry

Database: PDB / ID: 3br8

Title

Crystal structure of acylphosphatase from Bacillus subtilis

Components

Probable acylphosphatase

Keywords

HYDROLASE /

acylphosphatase / AcP / YflL

Function / homology

Function and homology information

acylphosphatase /

acylphosphatase activity
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.33 Å

Authors

Li, D. / Hu, J.C. / Xia, B. / Su, X.D.

Citation

Journal: to be published
Title: Conformational Transitions Revealed by Structures of Acylphosphatase from Bacillus subtilis in Different States
Authors: Hu, J.C. / Li, D. / Su, X.D. / Jin, C.W. / Xia, B.

History

Deposition	Dec 21, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 24, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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PDBx/mmCIF format	3br8.cif.gz	54.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3br8.ent.gz	39.9 KB	Display	PDB format
PDBx/mmJSON format	3br8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/3br8 ftp://data.pdbj.org/pub/pdb/validation_reports/br/3br8	HTTPS FTP

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Related structure data

Similar structure data	4nmo-1 4jop-2 2bjd-1 1poh-d 6qji-1 3cnr-2 6qji-2 4e35-1 4uu6-d 1y7n-d 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

Deposited unit

A: Probable acylphosphatase

hetero molecules

10.5 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)	26.857, 48.270, 59.567
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Probable acylphosphatase / Acylphosphate phosphohydrolase / YflL Mass: 10332.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yflL / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35031, acylphosphatase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.87 Å³/Da / Density % sol: 34.17 %
Crystal grow	Temperature: 277 K / Method: liquid diffusion / pH: 5.5 Details: 50mM phosphate buffer, pH 5.5, LIQUID DIFFUSION, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.1 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Highest resolution: 1.3 Å / Num. obs: 66430

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
CNS		refinement
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3.004	data extraction
HKL-2000		data collection
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.33→29.79 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.08 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	945	5.1 %	RANDOM
R_work	0.19	-	-	-
obs	0.192	18408	99.59 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 15.823 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	-0.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.33→29.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	702	0	11	105	818

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	736
X-RAY DIFFRACTION	r_angle_refined_deg	1.271	1.95	994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.139	5	93
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.587	23.611	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.651	15	124
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.042	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	107
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	559
X-RAY DIFFRACTION	r_nbd_refined	0.29	0.2	348
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	491
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.09	0.2	70
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.151	0.2	42
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.123	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.673	1.5	448
X-RAY DIFFRACTION	r_mcangle_it	1.043	2	720
X-RAY DIFFRACTION	r_scbond_it	1.222	3	288
X-RAY DIFFRACTION	r_scangle_it	1.684	4.5	272

LS refinement shell

Resolution: 1.329→1.364 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	74	-
R_work	0.33	1211	-
all	-	1285	-
obs	-	-	95.33 %

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	3.5526	0.6362	0.8594	3.9058	-0.8169	11.7927	-0.1633	0.2206	-0.5309	-0.1439	0.1223	-0.1467	0.3482	0.1412	0.0409	-0.0175	0.0206	0.0163	0.0309	-0.0095	0.0784	9.856	-2.44	33.392
2	3.7232	-3.9727	-3.191	11.7025	5.9831	6.4029	-0.1304	-0.0785	0.1454	0.6726	-0.0206	-0.1	0.0575	-0.0307	0.1509	0.0077	0.0072	-0.0325	0.047	0.0079	0.0338	4.059	5.785	47.622
3	1.0561	-0.6404	-0.0854	2.0845	0.6498	1.7798	-0.0554	-0.0212	-0.0349	0.1641	0.0736	0.0575	-0.0022	0.0561	-0.0182	-0.0052	0.0128	0.0092	0.0612	-0.0005	0.0658	-3.007	10.399	42.695
4	1.2582	-0.0259	-0.0023	1.3153	-0.3794	1.5813	-0.0017	0.0389	-0.0435	-0.0095	0.014	0.0371	0.046	-0.0369	-0.0122	0.0035	0.0006	0.0006	0.0631	0.006	0.0749	0.75	6.256	33.349
5	3.1841	-1.8765	1.6312	15.2473	2.7005	1.7838	-0.4333	-0.1633	-0.1444	1.6318	0.5089	0.785	0.6243	0.2478	-0.0756	0.1455	0.0647	0.0848	0.0143	0.0444	0.0124	-1.678	-0.786	49.664
6	3.0052	0.1044	-2.0399	0.2674	-1.3369	10.1481	-0.0902	-0.0101	-0.1946	-0.0617	0.0052	-0.044	0.3425	0.1413	0.085	-0.0003	0.007	0.0005	0.0338	0.0077	0.0729	3.006	0.161	37.386
7	2.4743	-0.1376	1.0124	1.8967	0.0822	2.6187	-0.0108	0.112	0.0041	0.0184	-0.0372	-0.121	-0.015	0.2095	0.048	-0.0068	-0.0059	0.0001	0.0843	0.0151	0.0794	11.544	7.118	32.674
8	10.2941	-6.4102	-6.6333	3.9917	4.1427	5.7411	0.0122	-0.0774	0.2769	-0.178	0.0417	-0.1542	-0.1983	0.2783	-0.0539	-0.0182	-0.0043	0.0021	0.0381	-0.0227	0.066	4.802	13.861	42.463
9	6.2555	-5.7784	-0.6806	17.9314	0.4855	0.6011	-0.1496	-0.313	0.2615	0.8808	0.3216	-1.1053	0.1137	0.1246	-0.172	0.0141	0.0352	-0.0733	0.0216	-0.0408	0.0664	4.134	12.355	49.153
10	9.2024	-8.5607	-8.3119	18.7987	21.2171	33.1447	-0.0397	-0.4955	0.0156	-0.1255	0.1615	-0.3477	-0.0712	0.2361	-0.1217	-0.0567	0.0225	-0.0082	0.068	0.0384	0.0793	11.824	-1.171	40.116
11	37.7157	-5.9782	13.4781	5.88	4.5078	13.7665	0.5394	0.1722	-1.9905	0.0274	-0.1343	0.1548	0.7483	-0.3545	-0.4051	-0.0385	-0.0348	0.0147	0.1055	-0.0795	0.2481	4.235	-5.598	28.044
12	13.2074	-1.8034	-5.6359	2.9881	0.3012	10.9263	-0.1264	0.1013	-0.4652	0.1479	-0.0445	0.2196	0.1915	-0.6402	0.1709	-0.0231	-0.0324	-0.0093	0.0486	0.0096	0.0857	-5.717	1.979	35.015

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	1 - 5	1 - 5
2	X-RAY DIFFRACTION	2	A	A	6 - 11	6 - 11
3	X-RAY DIFFRACTION	3	A	A	12 - 20	12 - 20
4	X-RAY DIFFRACTION	4	A	A	21 - 36	21 - 36
5	X-RAY DIFFRACTION	5	A	A	37 - 41	37 - 41
6	X-RAY DIFFRACTION	6	A	A	42 - 47	42 - 47
7	X-RAY DIFFRACTION	7	A	A	48 - 59	48 - 59
8	X-RAY DIFFRACTION	8	A	A	60 - 65	60 - 65
9	X-RAY DIFFRACTION	9	A	A	66 - 71	66 - 71
10	X-RAY DIFFRACTION	10	A	A	72 - 77	72 - 77
11	X-RAY DIFFRACTION	11	A	A	78 - 84	78 - 84
12	X-RAY DIFFRACTION	12	A	A	85 - 90	85 - 90

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