PDB-4eae: The crystal structure of a functionally unknown protein from List...

ID or keywords:

Entry

Database: PDB / ID: 4eae

Title

The crystal structure of a functionally unknown protein from Listeria monocytogenes EGD-e

Components

Lmo1068 protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Immunoglobulin-like - #4170 / Protein of unknown function DUF5068 / Domain of unknown function (DUF5068) / Immunoglobulin-like / Sandwich / Mainly Beta / D-MALATE / Lmo1068 protein

Function and homology information

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.32 Å

Authors

Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: The crystal structure of a functionally unknown protein from Listeria monocytogenes EGD-e
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Mar 22, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eae.cif.gz	165 KB	Display	PDBx/mmCIF format
PDB format	pdb4eae.ent.gz	138.9 KB	Display	PDB format
PDBx/mmJSON format	4eae.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eae_validation.pdf.gz	447 KB	Display	wwPDB validaton report
Full document	4eae_full_validation.pdf.gz	448.8 KB	Display
Data in XML	4eae_validation.xml.gz	21.5 KB	Display
Data in CIF	4eae_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/4eae ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4eae	HTTPS FTP

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Related structure data

Similar structure data	2hma-d 4gqo-1 4i59-3 1miq-2 2b11-1 1pfz-3 3ooa-2 1fqa-d 3d7z-d 3qvc-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP05677.3

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: Lmo1068 protein

B: Lmo1068 protein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	87.964, 87.964, 94.631
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Details

Experimentally unknown

#1: Protein	Lmo1068 protein Mass: 20551.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: Listeria monocytogenes, lmo1068 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8Y850
#2: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₅
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.57 Å³/Da / Density % sol: 52.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.1M DL-malic acid., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97901 Å / Relative weight: 1
Reflection	Resolution: 1.32→23 Å / Num. all: 97196 / Num. obs: 97196 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / R_merge(I) obs: 0.064 / Net I/σ(I): 43
Reflection shell	Resolution: 1.32→1.35 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4813 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
RESOLVE		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.32→22.593 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 16.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1773	4857	5 %	random
R_work	0.1582	-	-	-
all	0.1592	97106	-	-
obs	0.1592	97106	99.94 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.154 Å² / k_sol: 0.41 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3084 Å²	0 Å²	0 Å²
2-	-	-1.3084 Å²	-0 Å²
3-	-	-	2.6167 Å²

Refinement step

Cycle: LAST / Resolution: 1.32→22.593 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2829	0	20	539	3388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3030
X-RAY DIFFRACTION	f_angle_d	1.111	4137
X-RAY DIFFRACTION	f_dihedral_angle_d	10.804	1146
X-RAY DIFFRACTION	f_chiral_restr	0.075	471
X-RAY DIFFRACTION	f_plane_restr	0.005	539

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 (%)
1.3203-1.3353	0.2917	173	0.2841	3038	X-RAY DIFFRACTION	100
1.3353-1.351	0.3114	143	0.2652	3084	X-RAY DIFFRACTION	100
1.351-1.3675	0.2285	128	0.2427	3079	X-RAY DIFFRACTION	100
1.3675-1.3848	0.2689	147	0.2341	3082	X-RAY DIFFRACTION	100
1.3848-1.403	0.2388	175	0.2199	3070	X-RAY DIFFRACTION	100
1.403-1.4222	0.2431	164	0.1975	3070	X-RAY DIFFRACTION	100
1.4222-1.4425	0.2062	175	0.1984	3050	X-RAY DIFFRACTION	100
1.4425-1.464	0.1901	147	0.1844	3082	X-RAY DIFFRACTION	100
1.464-1.4869	0.2093	159	0.1755	3043	X-RAY DIFFRACTION	100
1.4869-1.5113	0.1733	171	0.1683	3070	X-RAY DIFFRACTION	100
1.5113-1.5373	0.1698	160	0.1591	3076	X-RAY DIFFRACTION	100
1.5373-1.5653	0.1709	160	0.1522	3058	X-RAY DIFFRACTION	100
1.5653-1.5954	0.1345	133	0.1503	3124	X-RAY DIFFRACTION	100
1.5954-1.6279	0.1696	187	0.1453	3035	X-RAY DIFFRACTION	100
1.6279-1.6633	0.1538	161	0.1429	3079	X-RAY DIFFRACTION	100
1.6633-1.702	0.1901	156	0.1491	3047	X-RAY DIFFRACTION	100
1.702-1.7446	0.1719	170	0.1526	3077	X-RAY DIFFRACTION	100
1.7446-1.7917	0.1607	174	0.1476	3075	X-RAY DIFFRACTION	100
1.7917-1.8444	0.1779	158	0.1504	3075	X-RAY DIFFRACTION	100
1.8444-1.9039	0.1638	154	0.1505	3089	X-RAY DIFFRACTION	100
1.9039-1.9719	0.1621	160	0.1492	3068	X-RAY DIFFRACTION	100
1.9719-2.0508	0.1667	163	0.1521	3076	X-RAY DIFFRACTION	100
2.0508-2.1441	0.1797	158	0.1492	3080	X-RAY DIFFRACTION	100
2.1441-2.257	0.1726	161	0.1483	3081	X-RAY DIFFRACTION	100
2.257-2.3983	0.1659	181	0.1512	3079	X-RAY DIFFRACTION	100
2.3983-2.5832	0.1826	171	0.1701	3081	X-RAY DIFFRACTION	100
2.5832-2.8428	0.1985	158	0.178	3069	X-RAY DIFFRACTION	100
2.8428-3.2531	0.1656	172	0.1586	3097	X-RAY DIFFRACTION	100
3.2531-4.0945	0.1545	171	0.1307	3083	X-RAY DIFFRACTION	100
4.0945-22.5966	0.1824	167	0.1513	3132	X-RAY DIFFRACTION	100

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	3.7489	-1.2611	-0.823	1.0145	0.7201	0.8951	0.0326	-0.2963	-0.5441	0.1484	-0.0495	0.0548	0.0877	0.0445	0.0362	0.1267	-0.0077	-0.0234	0.1615	0.0507	0.1665	51.8261	29.4436	40.7502
2	0.8448	0.4381	-0.1551	0.9976	-0.2126	0.8052	-0.0717	-0.0107	-0.1729	-0.0528	0.0094	-0.1525	0.0745	0.1399	0.0499	0.0927	-0.002	-0.0105	0.1207	0.006	0.1311	54.6923	29.954	26.9825
3	1.6067	1.2778	-0.4074	1.8526	-0.6682	1.2617	0.1566	-0.2742	0.1801	0.3565	-0.0758	0.1475	-0.1959	-0.022	-0.0348	0.1924	-0.0057	0.0325	0.1449	-0.0192	0.1362	40.6958	42.9318	40.42
4	0.4804	0.1612	-0.0928	0.7816	-0.015	1.3562	-0.0119	-0.0165	-0.0319	0.0354	0.0105	-0.1291	-0.1389	0.2023	0.0039	0.0947	-0.0286	-0.0107	0.1269	0.0002	0.1098	59.423	40.2194	28.6621
5	2.2688	-0.7856	-1.7047	1.8297	0.0771	3.2076	0.0451	0.176	-0.0754	-0.0424	0.0827	0.0652	0.179	-0.2438	-0.1275	0.1034	-0.012	-0.0129	0.1448	0.0159	0.1113	38.4837	34.953	23.6986
6	3.3777	2.0537	0.0329	2.0562	-0.1495	0.5374	-0.0761	0.2364	0.0535	-0.0722	0.099	-0.0413	-0.1885	0.1495	0.0011	0.1382	-0.0387	-0.006	0.1563	-0.0092	0.1072	56.7821	40.5376	17.7354
7	1.5966	-0.1899	0.6913	1.4101	0.4797	1.9245	-0.0658	0.1108	0.1847	-0.2696	-0.0493	-0.1314	-0.1852	0.3307	0.0306	0.1367	-0.0272	-0.0024	0.1389	0.0019	0.1543	57.2758	38.6831	15.9485
8	4.2701	-1.1806	-0.396	1.7885	0.416	0.3526	0.115	0.5181	0.1427	-0.3977	-0.1329	-0.2835	-0.0026	-0.0171	0.0237	0.1322	0.0205	0.0342	0.1624	0.0233	0.1257	50.9596	58.3002	-7.7323
9	1.229	-0.3708	-0.6026	0.7345	0.326	1.5353	0.0004	0.1818	-0.0674	-0.0107	-0.0549	0.0908	0.0472	-0.2749	0.0415	0.1398	-0.0122	0.0031	0.1453	-0.0121	0.1383	41.9581	50.2059	2.5088
10	0.9118	-0.606	-0.7079	1.4809	0.2156	1.0707	0.0351	-0.0467	0.212	-0.0892	0.0644	-0.3728	0.0266	0.1469	-0.0546	0.0594	-0.0004	0.0171	0.1082	-0.0295	0.1318	54.1864	52.2417	0.8266
11	0.616	0.2313	0.2708	1.3744	-0.1612	0.3855	-0.0211	-0.0657	0.1084	0.288	-0.0242	-0.0161	0.0175	-0.069	0.0108	0.1135	-0.0034	0.0036	0.1097	-0.0159	0.079	46.9945	54.2185	16.0157
12	0.4378	-0.2747	-0.157	1.7358	-0.4001	0.3346	0.0359	0.0837	0.0671	-0.003	0.0139	-0.2038	-0.0736	0.1807	0.0287	0.1193	-0.0087	0.0052	0.1234	-0.0067	0.1521	55.4951	59.1286	3.7974
13	1.1385	0.3738	-0.3026	0.6702	0.2339	1.0032	-0.0075	-0.0536	0.2477	-0.0007	0.0071	0.0106	-0.1615	0.032	-0.0122	0.1163	-0.0037	-0.0002	0.1	-0.0154	0.1253	47.2651	66.2885	13.053
14	0.8728	0.0485	-0.0784	1.4245	-0.6957	0.5093	-0.0113	-0.0437	-0.0283	0.1272	-0.0002	-0.0188	0.0065	-0.0097	0.0106	0.0925	-0.0056	-0.0041	0.0976	-0.013	0.0823	48.6429	48.1599	11.0542
15	1.1087	0.2839	-0.0837	1.1697	-0.4245	3.8284	-0.0664	-0.0477	-0.0764	0.0708	-0.0405	0.0617	-0.0154	-0.3413	-0.0403	0.091	0.0087	-0.0166	0.1076	-0.0033	0.1023	42.9508	44.4494	13.7699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 100:120)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 121:153)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 154:172)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 173:244)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 245:254)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 255:266)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 267:286)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 99:120)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 121:139)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 140:184)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 185:207)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 208:217)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 218:234)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 235:272)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 273:286)

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