PDB-4h1h: Crystal structure of MccF homolog from Listeria monocytogenes EGD-e

ID or keywords:

Entry

Database: PDB / ID: 4h1h

Title

Crystal structure of MccF homolog from Listeria monocytogenes EGD-e

Components

Lmo1638 protein

Keywords

HYDROLASE / MccF-like / CSGID / MccF homolog / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / SAD molecular replacement / Resolution: 2.46 Å

Authors

Nocek, B. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of MccF homolog from Listeria monocytogenes EGD-e
Authors: Nocek, B. / Tikhonov, A. / Severinov, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4h1h.cif.gz	257.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4h1h.ent.gz	223.3 KB	Display	PDB format
PDBx/mmJSON format	4h1h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4h1h_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	4h1h_full_validation.pdf.gz	463.5 KB	Display
Data in XML	4h1h_validation.xml.gz	25.9 KB	Display
Data in CIF	4h1h_validation.cif.gz	35.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/4h1h ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h1h	HTTPS FTP

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Related structure data

Related structure data	3gjz 4e5s
Similar structure data	4q05-d 3agb-d 3tyx-d 1ofr-4 3l21-3 4h7p-d 4e5s-1 4q3o-1 4gyj-1 6bq6-d 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-IDP91762

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Lmo1638 protein

B: Lmo1638 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: Lmo1638 protein

B: Lmo1638 protein

hetero molecules

A: Lmo1638 protein

B: Lmo1638 protein

hetero molecules

A: Lmo1638 protein

B: Lmo1638 protein

hetero molecules

defined by software
222 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	169.023, 169.023, 169.023
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	213
Space group name H-M	P4₁32

Components on special symmetry positions

ID	Model	Components
1	1	B-402- SO4
2	1	B-402- SO4

#1: Protein	Lmo1638 protein Mass: 36725.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo1638 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y6P6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.74 Å³/Da / Density % sol: 55.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.3 M Ammonium Sulfate, 0.2 Sodium Chloride, Acetate pH 4.5 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.45→40 Å / Num. all: 30740 / Num. obs: 30344 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / B_iso Wilson estimate: 59 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 17.7
Reflection shell	Resolution: 2.45→2.49 Å / % possible all: 99.8

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
Auto-Rickshaw		phasing
REFMAC	5.6.0117	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure: SAD molecular replacement / Resolution: 2.46→40 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.911 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 20.009 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.421 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25252	1533	5.1 %	RANDOM
R_work	0.20671	-	-	-
obs	0.20886	28799	98.83 %	-
all	-	30335	-	-

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 max: 143.84 Å² / B_iso mean: 42.848 Å² / B_iso min: 19.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.46→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4970	0	20	87	5077

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	5076
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	3298
X-RAY DIFFRACTION	r_angle_refined_deg	1.505	1.968	6892
X-RAY DIFFRACTION	r_angle_other_deg	3.34	3	8119
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.834	5	650
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.831	25.442	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.684	15	855
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.692	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	806
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5662
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	964

LS refinement shell

Resolution: 2.456→2.52 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.389	100	-
R_work	0.357	1894	-
obs	-	-	99.85 %

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	0.1934	0.3742	-0.3263	2.2274	-1.6297	1.2335	-0.2358	0.0119	-0.1926	-0.5172	0.0793	-0.078	0.3797	0.0244	0.1565	0.6511	-0.1606	-0.0011	0.3433	-0.0423	0.4833	171.1655	9.1981	35.2394
2	1.4161	-0.1083	-0.7031	2.0406	0.9926	0.8494	-0.094	-0.1597	0.113	-0.1785	0.0889	0.4044	-0.0335	0.0941	0.0051	0.506	0.0144	-0.074	0.2579	0.0364	0.5279	165.6598	27.6779	45.4826
3	0.1704	0.0922	-0.3059	1.1452	0.632	1.1543	-0.0341	-0.0361	0.0493	-0.3149	0.1651	0.075	-0.1128	0.1485	-0.131	0.5727	-0.0396	-0.088	0.2266	0.0476	0.4796	171.1384	28.3634	40.9351
4	1.4031	0.5671	0.3226	2.7269	-0.1556	0.1124	-0.3908	0.0226	0.2861	-0.5136	0.4072	0.334	-0.0802	-0.0522	-0.0164	0.6095	0.0453	-0.143	0.2345	0.066	0.6309	153.1591	26.6099	45.9696
5	15.2186	-1.9136	-5.444	0.4789	2.3556	13.746	0.4856	0.2198	0.2957	-0.1276	-0.0143	-0.0758	-0.4362	-0.1323	-0.4714	0.6787	-0.0444	-0.1658	0.2337	0.0411	0.4471	162.7617	19.4054	32.0937
6	0.8817	-0.0308	-0.5819	0.4145	-0.0284	1.0308	-0.1174	-0.0418	-0.0106	-0.1225	0.0736	0.0389	-0.1011	-0.1361	0.0437	0.4939	-0.0112	-0.0888	0.2822	0.0114	0.501	158.5103	14.8175	44.1853
7	1.0496	0.0551	1.1734	0.0066	0.0533	1.3477	-0.0117	0.0723	-0.0641	0.0414	0.0078	-0.0123	-0.0756	0.0204	0.0039	0.5235	-0.0528	-0.0208	0.3169	0.045	0.5106	173.3856	18.6339	48.6601
8	0.7415	1.5274	-0.7788	3.2447	-1.862	3.2186	-0.2135	0.0001	0.0829	-0.3436	-0.1017	0.0113	-0.0337	0.5262	0.3152	0.5143	-0.0571	-0.0076	0.3459	0.0322	0.4515	179.3386	9.4922	44.1897
9	3.914	-0.5887	-0.7104	5.8412	0.4983	0.1597	-0.125	-0.2053	-0.0536	-0.1158	0.0616	0.0194	-0.0026	0.0597	0.0634	0.5116	0.0202	-0.0319	0.3834	0.0741	0.4026	180.5445	16.1763	61.8392
10	8.7857	-0.9206	6.1094	3.6644	-2.5793	5.3266	-0.3227	-0.1383	0.3871	0.2011	0.096	-0.1283	-0.257	-0.1798	0.2268	0.5791	-0.0433	-0.0799	0.2715	0.016	0.4519	175.2192	29.5799	60.2242
11	0.9971	1.3592	1.0022	8.6506	1.9098	1.0788	-0.2536	0.119	-0.1317	0.0507	0.3562	-0.185	-0.1735	0.225	-0.1026	0.4569	-0.0105	-0.013	0.4123	0.0342	0.4155	182.0958	14.6147	64.1699
12	2.61	0.672	-1.682	4.3898	1.8906	22.0065	0.055	-0.1269	-0.3424	-0.0398	0.109	-0.2257	0.35	0.0814	-0.164	0.3925	0.0551	0.0739	0.2696	0.0564	0.4755	173.8264	-5.842	60.3448
13	0.4233	0.2638	0.3218	0.7677	-0.2111	0.5405	-0.1779	-0.0493	0.1348	-0.12	0.1131	0.0914	-0.0703	-0.102	0.0648	0.4502	0.039	0.0024	0.3612	-0.0045	0.5349	159.9139	6.6313	59.1503
14	24.5295	-7.0195	5.4609	4.7641	-1.154	1.2768	-0.5267	-0.5312	-0.0447	0.5288	0.5249	0.2508	-0.0573	-0.0557	0.0018	0.4447	0.0321	0.0496	0.3754	-0.0114	0.5019	158.372	-5.8874	56.5066
15	0.0566	-0.169	0.001	2.2002	-0.4807	0.1724	-0.0941	-0.0378	-0.0657	0.038	-0.0186	0.1412	-0.0235	0.0161	0.1127	0.4661	0.0466	-0.0012	0.3723	-0.0213	0.5436	169.7695	7.869	68.1214
16	10.624	0.1265	1.4374	7.1402	3.3476	7.4658	-0.0513	-0.6309	-0.0442	-0.2594	-0.3207	0.1627	0.4962	-0.3759	0.372	0.4021	0.0181	0.1134	0.3027	0.0818	0.4882	164.4384	-5.3576	67.4543
17	0.0582	0.0076	0.0016	0.0054	-0.0074	0.0155	-0.1045	0.029	0.0902	-0.0221	0.0482	-0.001	0.0304	-0.0564	0.0563	0.5172	0.0004	0.0083	0.3828	-0.007	0.5171	172.4438	7.9833	55.4416
18	3.1004	0.4103	3.8949	3.1602	-2.6768	8.3084	-0.1834	0.0551	-0.1437	-0.3646	-0.2811	-0.43	0.2159	0.255	0.4644	0.386	0.0153	0.1436	0.3224	-0.0116	0.5689	178.0519	-1.3482	51.3246
19	2.3061	0.8121	0.1795	0.6715	0.493	0.5092	0.0195	-0.0122	0.3443	0.0127	-0.0573	0.0933	-0.0395	-0.1113	0.0378	0.3036	0.1542	0.1311	0.5622	-0.095	0.5347	139.0833	2.7195	84.234
20	0.5757	0.918	-0.7519	1.884	-0.0711	4.3296	0.0048	-0.009	0.1633	0.189	-0.14	0.3285	-0.1477	-0.2257	0.1352	0.4583	0.2013	0.1921	0.4832	-0.184	0.6195	143.2666	11.155	93.8597
21	9.8011	-2.9685	-3.5732	1.1112	0.2959	4.2243	-0.1212	-0.3441	-0.097	0.0297	0.1096	0.025	0.0223	0.1027	0.0116	0.3619	0.1588	0.1945	0.569	-0.0781	0.4393	146.5234	-0.7116	90.928
22	0.2652	0.0082	0.2728	0.1765	0.2931	0.8156	0.091	0.1014	-0.0976	0.0892	-0.0951	0.044	0.0455	-0.1211	0.0041	0.4727	0.0783	0.0817	0.4698	-0.0305	0.5151	152.0594	-2.8576	81.308
23	0.5662	0.1279	0.4872	0.2397	-0.325	1.3517	-0.0901	-0.0535	0.1547	-0.1	0.0701	0.1076	0.0061	-0.1858	0.0201	0.347	0.0783	0.0897	0.474	-0.0178	0.5455	142.8372	0.2042	75.7954
24	1.9686	-6.1791	1.7854	19.6224	-5.7179	1.6779	-0.4332	-0.4356	0.0215	0.0939	0.8286	0.0626	0.0212	-0.2929	-0.3954	0.4146	0.2496	0.046	0.6607	0.0091	0.7494	134.951	4.2434	73.8659
25	9.0888	-3.8846	-5.1274	1.6705	2.2209	2.9791	-0.0702	-0.4407	-0.2624	-0.0505	0.092	0.075	-0.1717	0.0672	-0.0218	0.4689	0.4939	0.2109	0.6804	-0.0901	0.8297	143.2383	13.5255	87.0513
26	51.3359	28.0458	-14.8687	15.3249	-8.1143	4.3332	0.2768	-2.947	0.477	-0.2148	-0.9645	0.3164	0.0982	0.7698	0.6876	0.3397	0.4494	0.2367	0.8705	-0.1407	1.2675	137.4186	21.5412	87.7033
27	14.0756	12.5135	-4.8443	11.1284	-4.3081	1.6681	0.6032	-0.0141	0.8011	0.6271	-0.1839	0.7352	-0.2464	0.0223	-0.4193	0.1501	0.2493	0.0934	0.7124	-0.2174	0.7662	129.2858	11.8739	82.8482
28	21.8065	5.2725	2.742	2.5566	2.9288	4.3785	0.379	0.8866	0.4281	-0.1928	0.1287	-0.2499	-0.5537	-0.1866	-0.5077	0.466	0.4262	-0.015	0.4438	-0.1552	0.655	135.3752	24.089	78.6609
29	9.4422	3.3916	4.0576	8.1133	6.328	5.1997	-0.1618	-0.7016	0.7435	0.014	-0.4706	0.4034	-0.0084	-0.5646	0.6323	0.493	0.3147	0.1687	0.4468	-0.3168	0.848	150.0947	23.9584	89.2908
30	16.5442	10.5507	18.2086	10.8299	6.1388	29.5377	-1.7427	-0.8902	1.302	-0.6485	0.857	0.8632	-3.9257	-3.2456	0.8857	0.8588	0.6058	0.0491	0.6653	-0.1037	0.9247	135.5813	29.0218	70.7032
31	0.6348	-0.3215	-0.5091	0.2668	-0.0592	1.4669	0.0048	-0.2402	-0.0139	-0.0526	0.1666	0.0231	0.0104	-0.0903	-0.1713	0.337	0.0899	-0.001	0.416	-0.0516	0.6167	141.6453	9.3143	64.2174
32	1.626	0.4815	-0.103	0.9746	0.7312	0.7302	-0.131	0.0908	-0.1504	-0.1075	0.1577	-0.0711	-0.1093	0.0159	-0.0266	0.3824	0.1607	-0.0345	0.3565	-0.0022	0.637	146.5496	16.7489	60.1004
33	14.3334	3.3754	4.386	0.8133	1.346	7.4177	0.5992	0.5786	0.4084	0.1108	0.2342	0.06	-0.577	0.3802	-0.8335	0.5452	0.3928	0.0061	0.394	-0.1861	0.8346	141.4198	22.9282	69.279
34	8.5061	-0.4069	0.5486	0.8326	0.309	0.1757	-0.0527	-0.7075	0.38	-0.2518	-0.0349	0.0189	-0.1269	-0.1158	0.0876	0.5176	0.2843	-0.0374	0.3182	-0.0542	0.7039	147.0168	29.383	62.1694
35	3.49	1.3346	2.3023	2.5913	0.5714	1.5667	-0.4426	-0.1335	0.4804	-0.4101	0.2848	0.5735	-0.21	-0.1477	0.1577	0.31	0.2355	-0.087	0.4173	0.0501	0.7796	137.4932	22.8289	58.997
36	0.0859	-0.0789	0.1368	0.8625	-1.2963	1.9659	-0.1597	-0.2398	-0.0555	0.1311	0.4319	0.0966	-0.2246	-0.6856	-0.2722	0.235	0.4028	0.0744	0.8332	-0.0974	0.7623	131.9879	18.2385	72.2659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 9
2	X-RAY DIFFRACTION	2	A	10 - 28
3	X-RAY DIFFRACTION	3	A	29 - 51
4	X-RAY DIFFRACTION	4	A	52 - 68
5	X-RAY DIFFRACTION	5	A	69 - 77
6	X-RAY DIFFRACTION	6	A	78 - 124
7	X-RAY DIFFRACTION	7	A	125 - 146
8	X-RAY DIFFRACTION	8	A	147 - 163
9	X-RAY DIFFRACTION	9	A	164 - 171
10	X-RAY DIFFRACTION	10	A	172 - 179
11	X-RAY DIFFRACTION	11	A	180 - 190
12	X-RAY DIFFRACTION	12	A	191 - 197
13	X-RAY DIFFRACTION	13	A	198 - 248
14	X-RAY DIFFRACTION	14	A	249 - 254
15	X-RAY DIFFRACTION	15	A	255 - 276
16	X-RAY DIFFRACTION	16	A	277 - 285
17	X-RAY DIFFRACTION	17	A	286 - 309
18	X-RAY DIFFRACTION	18	A	310 - 324
19	X-RAY DIFFRACTION	19	B	0 - 22
20	X-RAY DIFFRACTION	20	B	23 - 41
21	X-RAY DIFFRACTION	21	B	42 - 50
22	X-RAY DIFFRACTION	22	B	51 - 73
23	X-RAY DIFFRACTION	23	B	74 - 124
24	X-RAY DIFFRACTION	24	B	125 - 130
25	X-RAY DIFFRACTION	25	B	131 - 140
26	X-RAY DIFFRACTION	26	B	141 - 147
27	X-RAY DIFFRACTION	27	B	148 - 158
28	X-RAY DIFFRACTION	28	B	159 - 171
29	X-RAY DIFFRACTION	29	B	172 - 180
30	X-RAY DIFFRACTION	30	B	181 - 197
31	X-RAY DIFFRACTION	31	B	198 - 229
32	X-RAY DIFFRACTION	32	B	230 - 255
33	X-RAY DIFFRACTION	33	B	256 - 263
34	X-RAY DIFFRACTION	34	B	264 - 277
35	X-RAY DIFFRACTION	35	B	278 - 293
36	X-RAY DIFFRACTION	36	B	294 - 324

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