PDB-4ose: X-ray Crystal Structure of a Putative Hydrolase from Rickettsia typhi

ID or keywords:

Entry

Database: PDB / ID: 4ose

Title

X-ray Crystal Structure of a Putative Hydrolase from Rickettsia typhi

Components

Putative Hydrolase

Keywords

HYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein

Function and homology information

Biological species

Rickettsia typhi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: X-ray Crystal Structure of a Putative Hydrolase from Rickettsia typhi
Authors: Fairman, J.W. / Abendroth, J. / Edwards, T.E. / Lorimer, D.

History

Deposition	Feb 12, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ose.cif.gz	236.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ose.ent.gz	189.9 KB	Display	PDB format
PDBx/mmJSON format	4ose.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ose_validation.pdf.gz	428.6 KB	Display	wwPDB validaton report
Full document	4ose_full_validation.pdf.gz	430.7 KB	Display
Data in XML	4ose_validation.xml.gz	21 KB	Display
Data in CIF	4ose_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/4ose ftp://data.pdbj.org/pub/pdb/validation_reports/os/4ose	HTTPS FTP

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Related structure data

Related structure data	3bwxS S: Starting model for refinement
Similar structure data	3p70-1 3bf6-d 4h6s-d 6s5m-d 2piz-3 2y5j-d 6fvp-d 1tws-2 1d4p-d 2zfq-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 - HomologyF&H Search
Other databases	TargetTrack: RityA.17523.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Putative Hydrolase

B: Putative Hydrolase

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

1

A: Putative Hydrolase

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

2

B: Putative Hydrolase

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

Unit cell

Length a, b, c (Å)	154.920, 49.060, 87.290
Angle α, β, γ (deg.)	90.000, 94.770, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	MET	MET	chain A	A	A	1 - 290	9 - 298
2	HIS	HIS	chain B	B	B	0 - 290	8 - 298

Details

AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

#1: Protein	Putative Hydrolase Mass: 34563.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia typhi (bacteria) / Strain: ATCC VR-144 / Wilmington / Gene: RT0431 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68WT4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.39 Å³/Da / Density % sol: 48.56 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 condition E3: 30% PEG 550 MME, 0.05 M Magnesium Chloride, 0.1 M HEPES pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.9787 Å

Detector

Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 28, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. all: 25980 / Num. obs: 25945 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 43.25 Å² / R_merge(I) obs: 0.061 / Χ²: 0.982 / Net I/σ(I): 16.74

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.4-2.46		0.518	2.53	8916	1916	99.7
2.46-2.53		0.487	2.77	8560	1838	100
2.53-2.6		0.354	3.71	8383	1802	99.8
2.6-2.68		0.3	4.48	8262	1769	99.9
2.68-2.77		0.265	5.09	7812	1685	100
2.77-2.87		0.191	6.82	7663	1648	99.9
2.87-2.98		0.173	8.11	7402	1585	100
2.98-3.1		0.12	11.03	7113	1537	99.9
3.1-3.24		0.092	13.97	6964	1493	99.8
3.24-3.39		0.072	17.47	6354	1370	100
3.39-3.58		0.056	22.24	6225	1346	99.8
3.58-3.79		0.049	26.16	5891	1282	100
3.79-4.06		0.04	31.25	5510	1197	100
4.06-4.38		0.034	35.09	5054	1110	100
4.38-4.8		0.032	38.38	4683	1030	99.7
4.8-5.37		0.032	37.71	4207	940	100
5.37-6.2		0.032	36.69	3665	829	99.9
6.2-7.59		0.031	38.86	3117	698	99.7
7.59-10.73		0.021	48.95	2351	552	99.6
	10.73	0.021	50.41	1240	318	95.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_1615	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3BWX

3bwx

Resolution: 2.4→43.494 Å / FOM work R set: 0.7871 / SU ML: 0.29 / σ(F): 1.36 / Phase error: 27.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2348	1314	5.07 %	RANDOM
R_work	0.2012	-	-	-
obs	0.2029	25907	99.74 %	-
all	-	25980	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 141.81 Å² / B_iso mean: 58.19 Å² / B_iso min: 23.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→43.494 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4384	0	0	71	4455

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4494
X-RAY DIFFRACTION	f_angle_d	0.656	6117
X-RAY DIFFRACTION	f_chiral_restr	0.024	694
X-RAY DIFFRACTION	f_plane_restr	0.003	771
X-RAY DIFFRACTION	f_dihedral_angle_d	12.596	1586

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2548	X-RAY DIFFRACTION	5.035	TORSIONAL
1	2	B	2548	X-RAY DIFFRACTION	5.035	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.4962	0.3019	130	0.2763	2713	2843	99
2.4962-2.6098	0.3165	144	0.2699	2692	2836	100
2.6098-2.7474	0.3348	140	0.2648	2723	2863	100
2.7474-2.9195	0.2938	142	0.2543	2724	2866	100
2.9195-3.1448	0.2943	154	0.2528	2704	2858	100
3.1448-3.4612	0.2521	148	0.226	2740	2888	100
3.4612-3.9617	0.2147	133	0.1876	2742	2875	100
3.9617-4.9902	0.1968	160	0.1562	2738	2898	100
4.9902-43.494	0.1957	163	0.1682	2817	2980	99

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	5.9873	-2.2156	0.1991	1.7515	-0.0149	2.9198	-0.2289	-0.9414	1.097	-0.0354	0.3141	-0.2007	-0.1461	-0.0608	-0.0605	0.3813	0.063	-0.0162	0.4896	-0.1793	0.5262	8.9221	59.1723	28.4562
2	7.5197	-0.1895	0.805	2.5949	0.0873	0.6982	-0.0032	-0.9463	0.7301	0.0307	0.0632	-0.0225	-0.1623	-0.0967	-0.0558	0.4087	0.0752	-0.0245	0.5485	-0.1175	0.4725	11.4463	56.0711	28.6697
3	3.5941	-0.8007	-0.3234	3.5132	-0.2662	2.0357	0.1257	0.3959	-0.0945	-0.0984	0.0603	-0.0996	0.0251	-0.2032	-0.1607	0.3312	0.008	-0.0341	0.493	-0.0529	0.3956	12.4246	52.5491	20.3314
4	6.8018	-0.3543	0.74	6.3518	1.6821	0.6073	0.1416	-0.0952	-0.7793	0.3492	-0.4369	0.3447	0.3218	-0.3396	0.3183	0.3561	0.007	0.0324	0.5776	-0.1154	0.4352	10.2877	42.1187	23.192
5	6.2093	0.4709	-3.6113	6.1909	0.7952	3.9146	-0.3691	-2.2426	-0.3849	0.8752	-0.2005	-0.1618	0.5277	-0.7381	0.6471	0.8195	0.1706	0.001	1.4466	0.1242	0.6111	16.4939	42.7263	48.2879
6	4.3478	-2.6282	-2.2482	6.0077	0.7966	3.5512	-0.6838	-1.3344	0.1305	0.5544	0.5631	-0.2389	0.223	0.2553	0.0678	0.501	0.1315	-0.0607	1.096	0.009	0.4214	22.8169	46.2804	40.7047
7	8.148	-4.9301	-4.6949	8.0006	0.5089	4.2961	-0.0932	-0.1825	-0.0163	0.6498	0.0109	-0.3424	0.6963	-0.1071	0.0062	0.5345	0.1101	-0	0.9565	-0.0257	0.3748	7.9221	50.0253	46.0911
8	7.7151	0.188	-0.7081	4.3268	-0.1888	4.5392	-0.0949	0.5672	-1.4473	-0.1702	-0.2636	0.3036	0.7739	-0.2179	0.3255	0.468	-0.01	0.0193	0.369	-0.1455	0.5946	14.6358	37.3508	17.9585
9	8.5241	3.2699	-3.1168	5.2401	-0.6103	6.192	-0.0584	-0.6623	-0.2284	0.2664	-0.2464	-0.0765	-0.1258	-0.386	0.1871	0.2747	0.1165	-0.0108	0.4996	0.0146	0.4034	27.4114	45.1643	24.2206
10	8.9675	-2.8262	-1.0882	2.4006	0.9322	4.6521	0.0269	-0.5919	0.8895	0.0963	0.1428	-0.5196	-0.2843	0.5042	-0.1854	0.3897	-0.0051	-0.0139	0.3293	-0.0291	0.472	59.7679	46.1202	20.2762
11	4.7139	-0.4539	0.1595	2.4164	0.6014	1.5139	0.0389	0.4268	0.1843	-0.5625	0.1122	-0.214	-0.0783	-0.022	-0.1738	0.4486	0.0726	0.0609	0.2826	-0.0142	0.3269	51.5222	44.2048	7.6611
12	2.6491	1.3538	-0.2643	0.8575	0.0175	3.0495	0.0778	0.429	1.2903	-0.0451	0.0077	-0.1366	-0.6001	-0.0008	-0.0871	0.6873	0.0419	0.131	0.4212	0.2303	0.9306	55.7747	58.3785	6.2945
13	6.4426	-1.056	-0.8996	4.3706	0.4459	4.7791	0.0977	0.1139	-0.6496	-0.4709	-0.0959	-0.0211	0.3998	-0.3518	-0.0234	0.3663	-0.0144	-0.0345	0.2387	0.0044	0.3524	42.5393	36.6067	13.0487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 48 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 100 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 101 through 122 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 123 through 154 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 155 through 172 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 173 through 194 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 195 through 209 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 210 through 264 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 265 through 290 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 112 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 113 through 180 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 181 through 209 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 210 through 290 )	B

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