PDB-4nvr: 2.22 Angstrom Resolution Crystal Structure of a Putative Acyltran...

ID or keywords:

Entry

Database: PDB / ID: 4nvr

Title

2.22 Angstrom Resolution Crystal Structure of a Putative Acyltransferase from Salmonella enterica

Components

Putative acyltransferase

Keywords

TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha/beta hydrolase family

Function / homology

Function and homology information

acyltransferase activity / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Salmonella enterica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.22 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Stam, J. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 2.22 Angstrom Resolution Crystal Structure of a Putative Acyltransferase from Salmonella enterica.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Stam, J. / Kwon, K. / Savchenko, A. / Anderson, W.F.

History

Deposition	Dec 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nvr.cif.gz	487.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4nvr.ent.gz	419.8 KB	Display	PDB format
PDBx/mmJSON format	4nvr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nvr_validation.pdf.gz	459.2 KB	Display	wwPDB validaton report
Full document	4nvr_full_validation.pdf.gz	469.5 KB	Display
Data in XML	4nvr_validation.xml.gz	49.3 KB	Display
Data in CIF	4nvr_validation.cif.gz	71 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nv/4nvr ftp://data.pdbj.org/pub/pdb/validation_reports/nv/4nvr	HTTPS FTP

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Related structure data

Similar structure data	2vaq-d 2fpb-d 4b9e-1 4iyg-d 3amp-d 6qhx-d 5l9e-2 2fpc-d 3r41-d 3amm-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	TargetTrack: CSGID-IDP01787

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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 acyltransferase

B: Putative acyltransferase

C: Putative acyltransferase

D: Putative acyltransferase

hetero molecules

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

1

A: Putative acyltransferase

C: Putative acyltransferase

hetero molecules

defined by author&software
69.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative acyltransferase

D: Putative acyltransferase

hetero molecules

defined by author&software
69.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.931, 71.380, 90.327
Angle α, β, γ (deg.)	113.03, 92.41, 90.09
Int Tables number	1
Space group name H-M	P1

#1: Protein	Putative acyltransferase Mass: 34542.230 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: MhpC, STM0332 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZRI7
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.06 Å³/Da / Density % sol: 40.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein: 8.8mg/mL, 0.3M Sodium cloride, 0.1M HEPES, pH 7.5. Screen: 0.2M Calcium acetate, 0.1M Na Cacodylate, pH 6.5, 9% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2009 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.22→30 Å / Num. all: 53580 / Num. obs: 53580 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / B_iso Wilson estimate: 27.3 Å² / R_merge(I) obs: 0.12 / R_sym value: 0.12 / Net I/σ(I): 19.4
Reflection shell	Resolution: 2.22→2.26 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.458 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2502 / R_sym value: 0.458 / % possible all: 92.3

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.8.0046	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.22→28.63 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.899 / SU B: 13.842 / SU ML: 0.18
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24143	2697	5.1 %	RANDOM
R_work	0.18125	-	-	-
obs	0.18431	50666	98.13 %	-
all	-	50666	-	-

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: 28.821 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	-1.03 Å²	0.02 Å²
2-	-	-1.82 Å²	0.36 Å²
3-	-	-	1 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→28.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9482	0	7	597	10086

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	9906
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9239
X-RAY DIFFRACTION	r_angle_refined_deg	1.566	1.958	13481
X-RAY DIFFRACTION	r_angle_other_deg	0.792	3	21245
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.178	5	1232
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.455	23.099	455
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.051	15	1484
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.681	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1463
X-RAY DIFFRACTION	r_gen_planes_refined	0.02	0.021	11342
X-RAY DIFFRACTION	r_gen_planes_other	0.017	0.02	2393
X-RAY DIFFRACTION	r_mcbond_it	1.312	1.267	4904
X-RAY DIFFRACTION	r_mcbond_other	1.312	1.267	4903
X-RAY DIFFRACTION	r_mcangle_it	1.394	1.894	6140
X-RAY DIFFRACTION	r_mcangle_other	1.394	1.894	6141
X-RAY DIFFRACTION	r_scbond_it	1.513	1.431	5002
X-RAY DIFFRACTION	r_scbond_other	1.513	1.431	5002
X-RAY DIFFRACTION	r_scangle_other	2.1	2.085	7341
X-RAY DIFFRACTION	r_long_range_B_refined	5.106	11.317	11884
X-RAY DIFFRACTION	r_long_range_B_other	5.002	11.049	11693

LS refinement shell

Resolution: 2.22→2.277 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	198	-
R_work	0.232	3600	-
obs	-	3600	94.5 %

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	9.672	-0.142	-0.8157	1.8978	-0.5699	3.3526	0.3974	-0.7031	-0.9321	0.4591	-0.4269	-0.5759	0.1123	0.1582	0.0295	0.4219	-0.0039	-0.1843	0.3884	0.11	0.346	45.5108	42.0117	99.5046
2	0.4618	0.3193	0.3967	1.0213	0.2172	1.7704	0.0551	-0.0838	-0.0205	0.0474	0.0431	0.0496	-0.1253	-0.2731	-0.0982	0.0779	0.0693	-0.0097	0.1397	-0.0071	0.0202	36.7255	44.5018	83.5337
3	1.6494	5.6195	-0.378	19.3131	-1.3339	0.1006	-0.6793	0.2972	0.691	-2.1196	0.7693	2.0362	0.0916	-0.0033	-0.09	0.7586	-0.1832	-0.536	0.8238	0.328	1.0679	52.0839	47.9482	73.333
4	0.4055	-0.1052	0.1442	0.8844	-0.1641	1.4978	-0.0208	-0	0.0338	-0.0235	0.1141	-0.0113	-0.349	-0.1897	-0.0932	0.1438	0.1015	0.0141	0.1515	-0.0171	0.0199	37.8853	51.9366	79.527
5	13.6364	-5.0468	4.1635	4.3516	-4.4935	6.9267	0.0113	0.5177	0.394	-0.4097	-0.1723	-0.4084	-0.0338	-0.1698	0.1611	0.2475	0.046	0.0873	0.2004	0.0173	0.0922	24.0089	-1.2089	35.4957
6	0.4155	-0.1496	-0.1825	1.0839	0.3305	1.8383	0.0333	0.066	0.035	-0.0309	-0.0056	0.0939	0.1051	-0.2115	-0.0276	0.0644	-0.0034	-0.0038	0.1163	-0.0184	0.0257	13.2809	-2.9221	50.7869
7	17.5616	-15.2731	-10.5632	13.727	9.027	6.4112	-1.5313	-0.658	-2.4402	1.3644	0.0719	2.0842	0.8814	0.5659	1.4594	0.5227	-0.0055	0.1351	0.5614	0.072	0.4886	28.198	-6.5665	61.7177
8	0.598	0.1477	-0.125	1.2215	0.1446	1.4423	0.0155	-0.0213	-0.0162	0.0597	0.02	0.0205	0.3297	-0.1668	-0.0355	0.1375	-0.0262	-0.0228	0.1294	-0.0299	0.0161	14.0616	-10.4804	55.526
9	4.6288	-0.6556	-0.6064	2.7611	1.1947	5.5986	0.0658	0.1297	-0.4956	-0.5502	0.1425	-0.7135	-0.0255	0.4885	-0.2083	0.2732	0.0462	0.0881	0.3654	-0.1237	0.3177	49.5639	18.7839	35.3913
10	0.7609	0.0486	-0.3616	3.2642	0.7984	4.7642	0.0709	0.1445	-0.1477	-0.4113	0.13	-0.1349	-0.0307	0.0054	-0.2008	0.1467	-0.0107	-0.0064	0.1421	-0.0586	0.0519	38.7052	19.6915	38.0152
11	0.3955	-0.1294	0.0988	1.0417	0.9033	1.7149	-0.0465	0.0895	-0.0329	-0.3147	0.1082	-0.0814	-0.4006	0.1292	-0.0618	0.1818	-0.04	0.0196	0.1042	-0.046	0.0229	40.3946	32.1824	47.3301
12	1.6233	-0.8395	0.2121	1.5364	0.2701	3.1776	0.0665	0.0273	-0.1094	-0.1638	-0.0724	0.3323	-0.4833	-0.4143	0.0059	0.2431	0.0591	-0.0773	0.2294	-0.0376	0.1014	24.4983	30.7558	43.6114
13	8.8823	-2.5953	4.8863	8.1526	-6.3467	21.3703	-0.055	0.105	-0.2265	-0.4926	0.255	0.3795	-0.2897	-0.5405	-0.2	0.1215	0.0245	-0.0693	0.114	-0.0667	0.0864	24.07	20.7205	34.6121
14	14.8227	-7.0097	11.6844	6.7053	-4.3473	9.9366	-0.0542	0.1745	-0.7983	0.1769	0.4942	-0.2056	-0.308	0.5204	-0.44	0.5116	-0.1214	-0.1717	0.4544	0.0545	0.6342	23.3873	28.8001	97.7793
15	1.5643	-0.4171	0.3203	1.3412	0.0733	3.7597	0.0176	-0.1167	0.213	0.2417	0.0522	-0.1881	-0.0134	0.2398	-0.0699	0.1361	0.0611	-0.0315	0.1416	-0.051	0.052	18.3174	20.4932	97.1967
16	0.8227	0.2738	-0.4325	0.8795	0.9892	1.9969	-0.0969	-0.0863	-0.0573	0.3276	0.0631	-0.054	0.6272	0.1033	0.0338	0.3024	0.1052	-0.01	0.1194	-0.0403	0.0284	15.7522	6.9418	89.7262
17	0.3628	-0.4879	-0.2298	1.1188	-0.0783	2.8689	-0.0398	-0.0454	0.0738	0.075	0.0802	-0.0402	0.4076	0.085	-0.0404	0.1276	0.0657	-0.0179	0.0915	-0.0415	0.0396	16.3277	12.4359	84.4455
18	1.1336	0.9814	0.2562	1.447	0.6572	3.4389	0.0775	0.0164	0.2053	0.1316	-0.0442	0.3927	0.6362	-0.4765	-0.0333	0.3007	-0.023	0.0308	0.3143	-0.0319	0.1571	0.2744	10.7185	90.7742
19	4.9694	1.7518	-1.7145	7.6688	-4.8538	20.2713	-0.0189	-0.0413	0.1181	0.6165	0.346	0.563	-0.4537	-0.8889	-0.3271	0.0895	0.0577	0.041	0.1629	-0.0408	0.0802	-0.2447	20.4873	100.1924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 22
2	X-RAY DIFFRACTION	2	A	23 - 185
3	X-RAY DIFFRACTION	3	A	186 - 198
4	X-RAY DIFFRACTION	4	A	199 - 304
5	X-RAY DIFFRACTION	5	B	3 - 15
6	X-RAY DIFFRACTION	6	B	16 - 185
7	X-RAY DIFFRACTION	7	B	186 - 198
8	X-RAY DIFFRACTION	8	B	199 - 304
9	X-RAY DIFFRACTION	9	C	4 - 29
10	X-RAY DIFFRACTION	10	C	30 - 72
11	X-RAY DIFFRACTION	11	C	73 - 242
12	X-RAY DIFFRACTION	12	C	243 - 289
13	X-RAY DIFFRACTION	13	C	290 - 304
14	X-RAY DIFFRACTION	14	D	4 - 14
15	X-RAY DIFFRACTION	15	D	15 - 79
16	X-RAY DIFFRACTION	16	D	80 - 182
17	X-RAY DIFFRACTION	17	D	183 - 243
18	X-RAY DIFFRACTION	18	D	244 - 289
19	X-RAY DIFFRACTION	19	D	290 - 304

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