PDB-3gkf: Crystal Structure of E. coli LsrF

ID or keywords:

Entry

Database: PDB / ID: 3gkf

Title

Crystal Structure of E. coli LsrF

Components

Aldolase lsrF

Keywords

LYASE /

TIM barrel /

Schiff base

Function / homology

Function and homology information

3-hydroxy-5-phosphooxypentane-2,4-dione thiolase /

fructose-bisphosphate aldolase activity / acyltransferase activity, transferring groups other than amino-acyl groups /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.9 Å

Authors

Miller, S.T. / Diaz, Z.C.

Citation

Journal: Plos One / Year: 2009
Title: The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
Authors: Diaz, Z. / Xavier, K.B. / Miller, S.T.

History

Deposition	Mar 10, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gkf.cif.gz	1002.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3gkf.ent.gz	841.3 KB	Display	PDB format
PDBx/mmJSON format	3gkf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/3gkf ftp://data.pdbj.org/pub/pdb/validation_reports/gk/3gkf	HTTPS FTP

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Related structure data

Related structure data	3glcC 3gndC C: citing same article (ref.)
Similar structure data	3gnd-2 3gnd-1 3glc-2 3glc-1 4p2v-d 5jm8-2 6ytf-d 2qji-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (4)

Deposited unit

O: Aldolase lsrF

L: Aldolase lsrF

M: Aldolase lsrF

N: Aldolase lsrF

K: Aldolase lsrF

F: Aldolase lsrF

I: Aldolase lsrF

H: Aldolase lsrF

G: Aldolase lsrF

J: Aldolase lsrF

S: Aldolase lsrF

P: Aldolase lsrF

Q: Aldolase lsrF

R: Aldolase lsrF

T: Aldolase lsrF

E: Aldolase lsrF

B: Aldolase lsrF

C: Aldolase lsrF

D: Aldolase lsrF

A: Aldolase lsrF

641 kDa, 20 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

O: Aldolase lsrF

L: Aldolase lsrF

M: Aldolase lsrF

N: Aldolase lsrF

K: Aldolase lsrF

S: Aldolase lsrF

P: Aldolase lsrF

Q: Aldolase lsrF

R: Aldolase lsrF

T: Aldolase lsrF

defined by author&software
321 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Aldolase lsrF

I: Aldolase lsrF

H: Aldolase lsrF

G: Aldolase lsrF

J: Aldolase lsrF

E: Aldolase lsrF

B: Aldolase lsrF

C: Aldolase lsrF

D: Aldolase lsrF

A: Aldolase lsrF

defined by author&software
321 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.501, 104.610, 171.673
Angle α, β, γ (deg.)	89.88, 79.31, 89.61
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999

Details

biological unit is a decamer. There are 2 biological units in the asymmetric unit (Chains ABCDEFGHIJ and chains KLMNOPQRST)

#1: Protein	Aldolase lsrF Mass: 32073.867 Da / Num. of mol.: 20 / Fragment: Uncharacterized aldolase LsrF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1517, JW1510, lsrF, yneB / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Aldolase lsrF

Mass: 32073.867 Da / Num. of mol.: 20 / Fragment: Uncharacterized aldolase LsrF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: b1517, JW1510, lsrF, yneB / Plasmid: pGEX-4T1 / Production host:

Escherichia coli (E. coli)
References: UniProt: P76143,

Lyases; Carbon-carbon lyases; Aldehyde-lyases

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.25 Å³/Da / Density % sol: 45.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 4% PEG 400, 100 mM MgCl2, 2.3 M Ammonium Sulfate, pH 7.5, vapor diffusion, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2008 / Details: Yale Mirrors

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.9→100 Å / Num. all: 178592 / Num. obs: 113378 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / B_iso Wilson estimate: 55.8 Å² / R_merge(I) obs: 0.092 / Χ²: 1.255 / Net I/σ(I): 9.057

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.9-3	1.7	0.361	10741	0.983	1	90.5
3-3.12	1.7	0.298	11017	1.061	1	92.9
3.12-3.27	1.8	0.221	11266	1.104	1	94.3
3.27-3.44	1.8	0.168	11262	1.187	1	95
3.44-3.65	1.8	0.129	11379	1.234	1	95.7
3.65-3.94	1.8	0.104	11485	1.282	1	96.4
3.94-4.33	1.8	0.075	11506	1.301	1	96.8
4.33-4.96	1.8	0.065	11604	1.32	1	97.5
4.96-6.25	1.8	0.066	11615	1.288	1	98
6.25-100	1.8	0.039	11503	1.686	1	96.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.5.0066	refinement
PDB_EXTRACT	3.006	data extraction
CrystalClear		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3GKF

3gkf

Resolution: 2.9→29.64 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 44.386 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	5685	5 %	RANDOM
R_work	0.209	-	-	-
obs	0.21	113374	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 96.34 Å² / B_iso mean: 36.968 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.19 Å²	1.9 Å²	0.85 Å²
2-	-	3.63 Å²	-3.18 Å²
3-	-	-	-1.77 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42300	0	0	241	42541

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	43060
X-RAY DIFFRACTION	r_angle_refined_deg	1.317	1.959	58220
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.475	5	5480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.301	23.871	1860
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.003	15	7440
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.308	15	320
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	6560
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	32380
X-RAY DIFFRACTION	r_mcbond_it	0.698	1.5	27380
X-RAY DIFFRACTION	r_mcangle_it	1.371	2	44000
X-RAY DIFFRACTION	r_scbond_it	1.825	3	15680
X-RAY DIFFRACTION	r_scangle_it	3.369	4.5	14220

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2115 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	TIGHT POSITIONAL	0.04	0.05
B	TIGHT POSITIONAL	0.04	0.05
C	TIGHT POSITIONAL	0.05	0.05
D	TIGHT POSITIONAL	0.04	0.05
E	TIGHT POSITIONAL	0.04	0.05
F	TIGHT POSITIONAL	0.04	0.05
G	TIGHT POSITIONAL	0.04	0.05
H	TIGHT POSITIONAL	0.05	0.05
I	TIGHT POSITIONAL	0.04	0.05
J	TIGHT POSITIONAL	0.04	0.05
K	TIGHT POSITIONAL	0.04	0.05
L	TIGHT POSITIONAL	0.04	0.05
M	TIGHT POSITIONAL	0.04	0.05
N	TIGHT POSITIONAL	0.05	0.05
O	TIGHT POSITIONAL	0.04	0.05
P	TIGHT POSITIONAL	0.04	0.05
Q	TIGHT POSITIONAL	0.04	0.05
R	TIGHT POSITIONAL	0.05	0.05
S	TIGHT POSITIONAL	0.04	0.05
T	TIGHT POSITIONAL	0.04	0.05
A	TIGHT THERMAL	0.07	0.5
B	TIGHT THERMAL	0.08	0.5
C	TIGHT THERMAL	0.08	0.5
D	TIGHT THERMAL	0.08	0.5
E	TIGHT THERMAL	0.07	0.5
F	TIGHT THERMAL	0.07	0.5
G	TIGHT THERMAL	0.08	0.5
H	TIGHT THERMAL	0.09	0.5
I	TIGHT THERMAL	0.08	0.5
J	TIGHT THERMAL	0.07	0.5
K	TIGHT THERMAL	0.07	0.5
L	TIGHT THERMAL	0.06	0.5
M	TIGHT THERMAL	0.07	0.5
N	TIGHT THERMAL	0.08	0.5
O	TIGHT THERMAL	0.07	0.5
P	TIGHT THERMAL	0.07	0.5
Q	TIGHT THERMAL	0.07	0.5
R	TIGHT THERMAL	0.09	0.5
S	TIGHT THERMAL	0.07	0.5
T	TIGHT THERMAL	0.08	0.5

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	379	-
R_work	0.34	7444	-
all	-	7823	-
obs	-	-	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	0.0908	0.1673	0.1176	0.3451	0.3711	0.8618	-0.0395	-0.0244	0.0848	-0.1083	-0.0547	0.1458	-0.3067	-0.0555	0.0942	0.27	-0.0241	-0.0778	0.0192	-0.0119	0.257	-14.205	34.3452	39.9106
2	0.934	-0.1392	-0.1378	0.3835	0.5228	1.0554	-0.0332	-0.314	-0.0368	0.0577	0.0304	-0.0683	0.1258	-0.0052	0.0027	0.069	-0.0686	-0.0165	0.2096	0.0363	0.0536	-8.9207	-10.0578	78.8911
3	0.8187	-0.0181	-0.179	0.0058	-0.0168	1.3139	-0.0986	-0.0945	-0.1532	0.0153	-0.0054	-0.0077	0.1466	0.0537	0.104	0.1024	-0.0151	0.0443	0.0275	0.0314	0.1218	-5.5035	-24.0341	45.0793
4	0.9819	0.5459	0.0294	1.1962	0.2559	0.4169	-0.1745	0.1092	0.1427	-0.1362	0.1058	-0.1397	-0.0959	-0.0384	0.0687	0.1412	-0.0635	-0.0192	0.0545	-0.0264	0.1206	-8.9729	3.3743	21.028
5	0.3057	0.0592	0.0756	0.38	-0.2616	0.7622	-0.0657	-0.2472	0.1386	0.0453	-0.0523	0.0241	-0.2245	-0.0915	0.1179	0.2175	0.0018	-0.0378	0.2427	-0.1713	0.2013	-14.2115	26.1289	75.6534
6	0.1024	-0.0287	-0.0374	0.2838	-0.189	0.697	0.023	0.1689	-0.0992	-0.0122	-0.0576	0.0023	0.0335	0.0319	0.0346	0.1082	0.0511	-0.0407	0.294	-0.176	0.1973	12.8463	30.117	-48.782
7	0.2114	0.0798	-0.0864	0.1906	-0.2333	1.0992	0.1088	0.1093	0.1731	-0.0281	0.0048	0.0267	-0.2603	0.1493	-0.1135	0.2438	-0.0005	0.1177	0.0983	0.0899	0.1718	20.5691	84.4061	-25.9143
8	0.9624	-0.3256	-0.111	0.782	-0.1054	0.371	0.0871	-0.0206	-0.1072	0.03	-0.0333	-0.1026	-0.106	0.0298	-0.0538	0.0754	-0.0144	-0.0057	0.0041	0.0052	0.0679	15.4627	60.8994	1.9052
9	0.2117	-0.2007	-0.2827	0.275	0.2366	0.7824	0.0128	0.0609	-0.1455	-0.0275	-0.0661	0.0711	0.0431	-0.0063	0.0533	0.0421	0.0114	-0.0243	0.0327	-0.06	0.2367	10.7591	27.4362	-12.1845
10	0.2686	0.1547	-0.0692	0.4963	0.2651	0.7286	0.05	0.2711	-0.0431	-0.014	0.0769	-0.1372	-0.13	-0.0805	-0.1269	0.1614	0.0894	0.0601	0.3277	0.005	0.0755	18.8933	65.3709	-57.2342
11	0.4201	-0.3081	-0.1474	0.5545	0.1645	0.5729	-0.0622	-0.2184	-0.0047	0.0886	0.0054	-0.0132	0.1719	-0.2736	0.0568	0.1182	-0.1271	0.001	0.4294	0.003	0.0531	39.9702	-20.7406	73.0806
12	0.6635	0.1267	0.1552	0.0353	0.096	0.6648	-0.0754	-0.133	0.2917	-0.0572	-0.0532	0.0394	-0.2946	-0.4338	0.1287	0.2392	0.1665	-0.0762	0.2957	-0.1189	0.3452	32.9206	31.6774	46.0324
13	0.7178	0.1634	0.1236	0.8143	0.028	0.4066	-0.1328	0.0991	0.1195	-0.1146	0.0546	0.0749	-0.0913	-0.2732	0.0782	0.1105	-0.0157	-0.0697	0.2674	0.0113	0.0885	37.7265	6.091	20.2218
14	0.9708	-0.1356	0.1142	0.1255	-0.2472	1.6992	-0.0095	-0.2358	-0.0566	-0.0695	0.0826	0.0086	0.2632	-0.4583	-0.073	0.1809	-0.1412	0.0404	0.2095	0.0009	0.0227	42.1427	-26.287	36.8999
15	0.6647	-0.2096	-0.0845	0.6894	-0.1522	0.4351	-0.0222	-0.2471	0.1759	-0.0133	0.0142	0.1052	-0.1538	-0.2313	0.008	0.1231	0.0427	-0.0162	0.4605	-0.1863	0.1231	34.3078	15.2075	78.7393
16	0.584	0.174	-0.0692	0.3537	0.277	0.4835	0.0764	0.4134	0.0439	-0.0878	-0.0328	0.0233	-0.1972	-0.2664	-0.0437	0.2549	0.1854	0.0492	0.502	0.1541	0.1314	-10.8549	76.7157	-54.9115
17	0.4644	0.0414	-0.3275	0.0696	0.1448	0.7768	0.0082	0.1817	-0.2253	-0.0154	-0.0339	-0.0264	0.007	-0.2398	0.0257	0.0766	0.0056	-0.0607	0.0973	-0.0836	0.275	-20.0874	29.1056	-20.5304
18	0.293	-0.0465	-0.2966	0.6059	0.2902	0.3993	0.0366	0.0998	-0.0359	-0.0639	-0.0606	0.0132	-0.0747	-0.115	0.0239	0.0346	0.024	0.0039	0.0422	0.0018	0.0367	-16.2741	58.3508	1.2694
19	0.5986	-0.132	0.1208	0.0666	-0.0942	0.9059	0.1353	0.2062	0.1552	-0.0608	-0.0265	-0.0509	-0.3187	-0.2082	-0.1087	0.2796	0.1482	0.1334	0.1435	0.1007	0.093	-10.6058	87.7482	-19.9035
20	0.5838	-0.1381	-0.4039	0.2718	0.0706	0.7343	0.0601	0.4494	-0.1254	0.0335	0.0196	0.0709	0.0216	-0.2088	-0.0797	0.0941	0.0697	-0.0498	0.4495	-0.1054	0.1069	-16.6364	40.434	-55.3154

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 290
2	X-RAY DIFFRACTION	1	A	292 - 302
3	X-RAY DIFFRACTION	2	B	10 - 290
4	X-RAY DIFFRACTION	2	B	292 - 301
5	X-RAY DIFFRACTION	3	C	10 - 290
6	X-RAY DIFFRACTION	3	C	292 - 326
7	X-RAY DIFFRACTION	4	D	10 - 290
8	X-RAY DIFFRACTION	4	D	292 - 309
9	X-RAY DIFFRACTION	5	E	10 - 290
10	X-RAY DIFFRACTION	5	E	292 - 297
11	X-RAY DIFFRACTION	6	F	10 - 290
12	X-RAY DIFFRACTION	6	F	292 - 300
13	X-RAY DIFFRACTION	7	G	10 - 290
14	X-RAY DIFFRACTION	7	G	292 - 307
15	X-RAY DIFFRACTION	8	H	10 - 290
16	X-RAY DIFFRACTION	8	H	292 - 311
17	X-RAY DIFFRACTION	9	I	10 - 290
18	X-RAY DIFFRACTION	9	I	292 - 300
19	X-RAY DIFFRACTION	10	J	10 - 290
20	X-RAY DIFFRACTION	10	J	292 - 301
21	X-RAY DIFFRACTION	11	K	10 - 290
22	X-RAY DIFFRACTION	11	K	292 - 297
23	X-RAY DIFFRACTION	12	L	10 - 290
24	X-RAY DIFFRACTION	12	L	292 - 302
25	X-RAY DIFFRACTION	13	M	10 - 290
26	X-RAY DIFFRACTION	13	M	292 - 304
27	X-RAY DIFFRACTION	14	N	10 - 290
28	X-RAY DIFFRACTION	14	N	292 - 307
29	X-RAY DIFFRACTION	15	O	10 - 290
30	X-RAY DIFFRACTION	15	O	292 - 304
31	X-RAY DIFFRACTION	16	P	10 - 290
32	X-RAY DIFFRACTION	16	P	292 - 296
33	X-RAY DIFFRACTION	17	Q	10 - 290
34	X-RAY DIFFRACTION	17	Q	292 - 301
35	X-RAY DIFFRACTION	18	R	10 - 290
36	X-RAY DIFFRACTION	18	R	292 - 297
37	X-RAY DIFFRACTION	19	S	10 - 290
38	X-RAY DIFFRACTION	19	S	292 - 301
39	X-RAY DIFFRACTION	20	T	10 - 290
40	X-RAY DIFFRACTION	20	T	292 - 298

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