PDB-2hv2: Crystal Structure of Conserved Protein of Unknown Function from E...

ID or keywords:

Entry

Database: PDB / ID: 2hv2

Title

Crystal Structure of Conserved Protein of Unknown Function from Enterococcus faecalis V583 at 2.4 A Resolution, Probable N-Acyltransferase

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG

Function / homology

Function and homology information

N-acetyltransferase activity
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4 Å

Authors

Tereshko, V.A. / Qiu, Y. / Kossiakoff, A.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of conserved hypothetical protein from Enterococcus faecalis V583 at 2.4 A resolution.
Authors: Qiu, Y. / Tereshko, V.A. / Kossiakoff, A.A. / Joachimiak, A.

History

Deposition	Jul 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2hv2.cif.gz	474.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2hv2.ent.gz	407.6 KB	Display	PDB format
PDBx/mmJSON format	2hv2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2hv2_validation.pdf.gz	496.4 KB	Display	wwPDB validaton report
Full document	2hv2_full_validation.pdf.gz	535.7 KB	Display
Data in XML	2hv2_validation.xml.gz	87.6 KB	Display
Data in CIF	2hv2_validation.cif.gz	119.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hv/2hv2 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/2hv2	HTTPS FTP

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Related structure data

Similar structure data	4my3-d 3n7z-d 6rfy-d 1k93-d 2ozg-1 1s26-d 4my0-d 6rfx-d 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	TargetDB: APC28944

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (9) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

C: Hypothetical protein

D: Hypothetical protein

E: Hypothetical protein

F: Hypothetical protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	189.626, 104.277, 152.281
Angle α, β, γ (deg.)	90.00, 98.26, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	A
8	1	B
9	1	C
10	1	D
11	1	E
12	1	F

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	ALA	A	A	4 - 337	7 - 340
2	1	LYS	ALA	B	B	4 - 337	7 - 340
3	1	LYS	ALA	C	C	4 - 337	7 - 340
4	1	LYS	ALA	D	D	4 - 337	7 - 340
5	1	LYS	ALA	E	E	4 - 337	7 - 340
6	1	LYS	ALA	F	F	4 - 337	7 - 340
7	2	ALA	TYR	A	A	344 - 396	347 - 399
8	2	ALA	TYR	B	B	344 - 396	347 - 399
9	2	ALA	TYR	C	C	344 - 396	347 - 399
10	2	ALA	TYR	D	D	344 - 396	347 - 399
11	2	ALA	TYR	E	E	344 - 396	347 - 399
12	2	ALA	TYR	F	F	344 - 396	347 - 399

Details

There are six protein molecules in the asymmetric unit. Oligomerization is unknown.

#1: Protein	Hypothetical protein Mass: 46251.285 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q836T6
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.44 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97929 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2006

Radiation

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

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. all: 112275 / Num. obs: 112275 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.095 / Net I/σ(I): 9.43

Reflection shell

Resolution: 2.4→2.49 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 1.23 / % possible all: 87.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.4→20 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.931 / SU B: 18.547 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.384 / ESU R Free: 0.247
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23347	5613	5 %	RANDOM
R_work	0.18504	-	-	-
all	0.18751	106381	-	-
obs	0.18751	106381	97.91 %	-

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: 33.891 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.53 Å²	0 Å²	2.45 Å²
2-	-	-1.97 Å²	0 Å²
3-	-	-	1.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18993	0	153	541	19687

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	19626
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	13538
X-RAY DIFFRACTION	r_angle_refined_deg	1.404	1.891	26524
X-RAY DIFFRACTION	r_angle_other_deg	0.864	2.179	32811
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.955	5	2337
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.697	23.91	936
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.784	15	3321
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.204	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2760
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	21675
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4203
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	3601
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	13204
X-RAY DIFFRACTION	r_nbtor_refined	0.199	0.2	9335
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	9242
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	540
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	0.261	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.262	0.2	23
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.197	0.2	6
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	1.058	1.5	14720
X-RAY DIFFRACTION	r_mcbond_other	0.153	1.5	4782
X-RAY DIFFRACTION	r_mcangle_it	1.079	2	18721
X-RAY DIFFRACTION	r_scbond_it	1.933	3	9317
X-RAY DIFFRACTION	r_scangle_it	2.79	4.5	7803
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2277	medium positional	0.27	0.5
2	B	2277	medium positional	0.26	0.5
3	C	2277	medium positional	0.38	0.5
4	D	2277	medium positional	0.23	0.5
5	E	2277	medium positional	0.19	0.5
6	F	2277	medium positional	0.35	0.5
1	A	3057	loose positional	0.59	5
2	B	3057	loose positional	0.69	5
3	C	3057	loose positional	0.63	5
4	D	3057	loose positional	0.6	5
5	E	3057	loose positional	0.55	5
6	F	3057	loose positional	0.71	5
1	A	2277	medium thermal	0.46	2
2	B	2277	medium thermal	0.51	2
3	C	2277	medium thermal	0.53	2
4	D	2277	medium thermal	0.48	2
5	E	2277	medium thermal	0.54	2
6	F	2277	medium thermal	0.44	2
1	A	3057	loose thermal	1.08	10
2	B	3057	loose thermal	1.13	10
3	C	3057	loose thermal	1.19	10
4	D	3057	loose thermal	1.08	10
5	E	3057	loose thermal	1.22	10
6	F	3057	loose thermal	1.16	10

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	376	-
R_work	0.261	6574	-
obs	-	-	83.49 %

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	0.8759	0.0269	0.2149	0.914	0.0286	0.9457	0.0214	0.0401	0.1554	-0.0551	0.024	-0.2332	-0.1106	0.0123	-0.0454	0.0438	-0.0092	0.0459	-0.151	0.0058	-0.0378	49.9045	19.3027	40.0044
2	0.7335	-0.3461	-0.0778	0.7329	-0.0058	0.6746	-0.0095	-0.0686	0.0124	0.0898	0.0252	-0.0153	-0.0188	-0.0074	-0.0156	0.043	-0.0026	0.015	-0.0956	0.0088	-0.1538	32.3928	0.8369	64.8511
3	0.5231	-0.0814	-0.1332	0.9947	0.1768	0.8373	0.0382	0.0266	0.0347	0.0777	0.0634	-0.0341	-0.0412	0.1287	-0.1016	-0.1864	-0.03	-0.0114	-0.0553	-0.0204	-0.1097	72.0036	-23.0928	15.615
4	0.5898	-0.0023	-0.1307	0.8727	-0.0357	1.1701	-0.0446	-0.118	-0.0264	0.2027	0.0773	-0.1532	0.0764	0.2939	-0.0327	-0.0369	0.0548	-0.0701	0.0443	0.0098	-0.079	73.6416	-30.2852	50.5223
5	0.762	-0.2554	-0.0608	0.9029	-0.1113	0.4422	0.0158	0.1264	-0.1307	0.0632	-0.044	0.1683	0.0124	-0.1374	0.0282	-0.1755	-0.0176	-0.0258	0.0065	0.0271	-0.0934	19.1476	-15.4486	12.7533
6	0.4129	-0.0852	0.0077	0.6104	0.1342	0.9188	-0.0371	0.0307	-0.1559	0.1667	-0.0097	0.1042	0.0964	-0.0368	0.0468	-0.0621	-0.0644	0.0503	-0.0978	0.0423	0.0251	23.2949	-43.1723	34.8818

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 397	5 - 400
2	X-RAY DIFFRACTION	1	A	G	701	1
3	X-RAY DIFFRACTION	1	A	L	801	1
4	X-RAY DIFFRACTION	1	A	R	802 - 883	1 - 82
5	X-RAY DIFFRACTION	2	B	B	1 - 397	4 - 400
6	X-RAY DIFFRACTION	2	B	H	702	1
7	X-RAY DIFFRACTION	2	B	M	802	1
8	X-RAY DIFFRACTION	2	B	S	808 - 896	6 - 94
9	X-RAY DIFFRACTION	3	C	C	1 - 397	4 - 400
10	X-RAY DIFFRACTION	3	C	I	703	1
11	X-RAY DIFFRACTION	3	C	N	803	1
12	X-RAY DIFFRACTION	3	C	T	805 - 897	2 - 94
13	X-RAY DIFFRACTION	4	D	D	2 - 397	5 - 400
14	X-RAY DIFFRACTION	4	D	J	704	1
15	X-RAY DIFFRACTION	4	D	O	804	1
16	X-RAY DIFFRACTION	4	D	U	810 - 881	6 - 77
17	X-RAY DIFFRACTION	5	E	E	1 - 397	4 - 400
18	X-RAY DIFFRACTION	5	E	K	705	1
19	X-RAY DIFFRACTION	5	E	P	805	1
20	X-RAY DIFFRACTION	5	E	V	812 - 902	7 - 97
21	X-RAY DIFFRACTION	6	F	F	1 - 397	4 - 400
22	X-RAY DIFFRACTION	6	F	Q	806	1
23	X-RAY DIFFRACTION	6	F	W	814 - 894	8 - 88

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