PDB-4yf1: 1.85 angstrom crystal structure of lmo0812 from Listeria monocyto...

ID or keywords:

Entry

Database: PDB / ID: 4yf1

Title

1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e

Components

Lmo0812 protein

Keywords

HYDROLASE / putative pyrophosphohydrolase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

HD domain / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / HD domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / CITRATE ANION / Lmo0812 protein

Function and homology information

Biological species

Listeria monocytogenes serovar 1/2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Krishna, S.N. / Light, S.H. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: 1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e
Authors: Krishna, S.N. / Light, S.H. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Feb 24, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yf1.cif.gz	272.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4yf1.ent.gz	229.3 KB	Display	PDB format
PDBx/mmJSON format	4yf1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4yf1_validation.pdf.gz	470.8 KB	Display	wwPDB validaton report
Full document	4yf1_full_validation.pdf.gz	475.1 KB	Display
Data in XML	4yf1_validation.xml.gz	29.1 KB	Display
Data in CIF	4yf1_validation.cif.gz	43.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yf/4yf1 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yf1	HTTPS FTP

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Related structure data

Similar structure data	1hjr-1 6zxv-2 3o2y-d 6iru-1 1usn-3 3hch-d 3s8j-d 5idq-d 2x4m-3 4bzp-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: MCSG-APC106841

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (2)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Lmo0812 protein

B: Lmo0812 protein

C: Lmo0812 protein

D: Lmo0812 protein

hetero molecules

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

1

A: Lmo0812 protein

C: Lmo0812 protein

hetero molecules

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

2

B: Lmo0812 protein

D: Lmo0812 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.811, 58.675, 95.730
Angle α, β, γ (deg.)	90.00, 114.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lmo0812 protein Mass: 22046.979 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8T2
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.55 Å³/Da / Density % sol: 51.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M tri-sodium citrate, pH 5.5, 20% (w/v) PEG 3000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. obs: 75985 / % possible obs: 99.2 % / Redundancy: 6.5 % / R_merge(I) obs: 0.085 / Net I/σ(I): 31.6
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.643 / Mean I/σ(I) obs: 2.36 / Num. unique all: 3546 / % possible all: 92.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→29.34 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.954 / SU B: 6.428 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20801	3735	5 %	RANDOM
R_work	0.18028	-	-	-
obs	0.18164	71643	99.05 %	-

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: 34.102 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.4 Å²	0 Å²	0.08 Å²
2-	-	-2.83 Å²	-0 Å²
3-	-	-	-1.16 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→29.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4997	0	15	508	5520

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	5242
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4961
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.949	7107
X-RAY DIFFRACTION	r_angle_other_deg	0.883	3	11413
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.606	5	634
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.526	24.052	269
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.371	15	902
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.835	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	766
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	5947
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	1247
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.336	2.066	2503
X-RAY DIFFRACTION	r_mcbond_other	1.336	2.065	2502
X-RAY DIFFRACTION	r_mcangle_it	2.185	3.078	3133
X-RAY DIFFRACTION	r_mcangle_other	2.185	3.079	3134
X-RAY DIFFRACTION	r_scbond_it	1.779	2.342	2739
X-RAY DIFFRACTION	r_scbond_other	1.776	2.341	2737
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.961	3.422	3969
X-RAY DIFFRACTION	r_long_range_B_refined	6.836	18.181	6476
X-RAY DIFFRACTION	r_long_range_B_other	6.498	17.245	6233
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	262	-
R_work	0.29	4935	-
obs	-	-	93.17 %

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	0.7481	-0.5359	-0.1082	3.2446	-0.6703	1.0923	0.0427	-0.0244	0.0043	-0.3783	-0.0201	-0.0063	-0.1138	-0.0121	-0.0226	0.1042	0.0038	-0.0408	0.1282	-0.015	0.1548	-44.66	-6.0906	-8.5981
2	4.272	1.1446	-2.1661	2.3796	-0.0793	3.8887	0.2608	0.2588	0.0438	0.0406	-0.1484	-0.1819	-0.244	-0.005	-0.1124	0.027	0.0207	-0.024	0.1385	0.0064	0.1782	-35.2581	5.5441	1.659
3	1.8254	0.0446	-0.0878	1.8932	-0.0372	1.0137	-0.0626	-0.0124	-0.1354	-0.0173	-0.0028	-0.2015	0.0931	0.1079	0.0654	0.0197	-0.0009	-0.0286	0.1383	0.0057	0.222	-32.318	-6.6871	4.8556
4	6.7387	-0.3496	-0.7858	2.161	-0.3486	1.3441	0.1797	-0.1941	-0.1011	0.1793	-0.1653	-0.0196	0.2368	-0.0391	-0.0143	0.0969	-0.0372	-0.0275	0.0662	0.0141	0.122	-38.3279	-12.1094	9.9284
5	0.6708	-0.2693	0.4967	2.9066	0.1654	1.2701	0.0356	0.0118	-0.0228	-0.3083	-0.0201	0.025	0.1645	-0.0191	-0.0155	0.0839	-0.0092	0.0385	0.1052	0.0084	0.1223	-0.3434	14.7071	-8.6518
6	1.2208	0	0.3641	3.0659	-0.3633	1.1858	0.1067	0.0244	-0.0682	-0.0645	-0.0602	0.0998	-0.0548	-0.0046	-0.0465	0.0241	-0.0046	0.0159	0.1246	-0.0031	0.1277	-6.2533	8.7745	2.4117
7	4.9536	-0.6008	1.5876	1.6651	-0.1412	1.4038	0.0036	-0.0862	0.2307	0.0564	-0.0203	0.1623	-0.0906	-0.1248	0.0167	0.0195	-0.0038	0.0331	0.0927	0.0054	0.1124	-14.1229	14.2599	6.8426
8	6.4288	-0.2738	0.4058	1.7873	-0.2346	1.8776	0.1536	-0.0129	0.147	0.2186	-0.0866	-0.0879	-0.1949	0.0042	-0.0671	0.0648	-0.0268	0.0298	0.0334	-0.0149	0.0717	-5.9042	20.76	10.5521
9	2.724	1.6238	-0.0601	3.065	0.3404	1.4547	-0.0642	0.0867	0.0583	-0.3321	0.0632	-0.1154	-0.2717	0.0568	0.0009	0.1458	0.0197	-0.0407	0.0754	0.0061	0.0752	-46.6659	-11.4168	-19.8064
10	0.684	0.5241	0.3988	1.1368	-1.0104	2.8125	-0.012	0.0313	0.0446	0.0837	-0.0311	-0.0658	-0.1833	0.1378	0.0431	0.0585	0.0146	-0.0193	0.1353	-0.002	0.1375	-55.075	-11.9894	-31.0213
11	13.3317	2.3252	-7.0972	6.5929	-3.353	12.1312	-0.2315	-0.2813	0.1306	-0.1518	0.0745	-0.105	-0.0131	0.1847	0.157	0.1417	0.0142	-0.0096	0.012	-0.01	0.0335	-67.3213	-2.0184	-28.2144
12	1.4562	-0.5068	-0.5006	2.7189	-0.0842	2.7171	0.1398	0.0456	-0.0506	-0.0756	0.0122	0.2445	0.1382	-0.1245	-0.1519	0.0283	-0.0127	-0.0224	0.111	0.0198	0.0532	-63.4484	-16.5645	-31.3496
13	2.5333	1.4101	-0.4006	2.7615	-0.9072	1.791	-0.0592	0.0937	-0.1174	-0.1465	0.0578	0.0657	0.291	-0.0701	0.0014	0.1229	0.0069	0.025	0.0471	-0.0197	0.0346	1.1011	20.2	-19.7419
14	0.3002	0.3814	-0.5102	1.0892	0.4102	3.4168	-0.0176	0.0299	-0.0346	0.0485	-0.0377	0.0485	0.1675	-0.1276	0.0553	0.0391	-0.0029	0.0138	0.1141	-0.0154	0.0692	6.6573	21.1748	-32.6716
15	3.8604	0.1715	0.9276	0.9057	0.0865	6.1888	-0.0522	-0.2627	-0.6598	0.1776	0.0558	-0.151	0.6118	0.2918	-0.0036	0.221	0.0836	-0.0139	0.206	0.003	0.2857	22.2155	10.4625	-33.1015
16	1.734	-0.2825	-0.1916	3.0348	1.3003	2.5003	0.1564	0.0539	0.0478	-0.0552	0.0377	-0.2134	-0.0575	0.1931	-0.1941	0.0213	-0.023	0.0108	0.1133	-0.0209	0.0299	16.0531	27.0341	-33.3446

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 80
2	X-RAY DIFFRACTION	2	A	81 - 102
3	X-RAY DIFFRACTION	3	A	103 - 158
4	X-RAY DIFFRACTION	4	A	159 - 179
5	X-RAY DIFFRACTION	5	B	19 - 81
6	X-RAY DIFFRACTION	6	B	82 - 121
7	X-RAY DIFFRACTION	7	B	122 - 158
8	X-RAY DIFFRACTION	8	B	159 - 180
9	X-RAY DIFFRACTION	9	C	27 - 82
10	X-RAY DIFFRACTION	10	C	83 - 125
11	X-RAY DIFFRACTION	11	C	126 - 137
12	X-RAY DIFFRACTION	12	C	138 - 180
13	X-RAY DIFFRACTION	13	D	27 - 81
14	X-RAY DIFFRACTION	14	D	82 - 122
15	X-RAY DIFFRACTION	15	D	123 - 140
16	X-RAY DIFFRACTION	16	D	141 - 180

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