PDB-3gnd: Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate

ID or keywords:

Entry

Database: PDB / ID: 3gnd

Title

Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate

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 /

SYNCHROTRON /

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 17, 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	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gnd.cif.gz	1020.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3gnd_validation.pdf.gz	614.7 KB	Display	wwPDB validaton report
Full document	3gnd_full_validation.pdf.gz	714.7 KB	Display
Data in XML	3gnd_validation.xml.gz	200.7 KB	Display
Data in CIF	3gnd_validation.cif.gz	253.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnd ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnd	HTTPS FTP

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Related structure data

Related structure data	3gkfSC 3glcC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3gkf-1 4p2v-d 3glc-2 3glc-1 3gkf-2 5jm8-2 5w1x-2 6wvv-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

A: Aldolase lsrF

B: Aldolase lsrF

C: Aldolase lsrF

D: Aldolase lsrF

E: Aldolase lsrF

F: Aldolase lsrF

G: Aldolase lsrF

H: Aldolase lsrF

I: Aldolase lsrF

J: Aldolase lsrF

K: Aldolase lsrF

L: Aldolase lsrF

M: Aldolase lsrF

N: Aldolase lsrF

O: Aldolase lsrF

P: Aldolase lsrF

Q: Aldolase lsrF

R: Aldolase lsrF

S: Aldolase lsrF

T: Aldolase lsrF

hetero molecules

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

1

A: Aldolase lsrF

B: Aldolase lsrF

C: Aldolase lsrF

D: Aldolase lsrF

E: Aldolase lsrF

F: Aldolase lsrF

G: Aldolase lsrF

H: Aldolase lsrF

I: Aldolase lsrF

J: Aldolase lsrF

hetero molecules

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

2

K: Aldolase lsrF

L: Aldolase lsrF

M: Aldolase lsrF

N: Aldolase lsrF

O: Aldolase lsrF

hetero molecules

P: Aldolase lsrF

Q: Aldolase lsrF

R: Aldolase lsrF

S: Aldolase lsrF

T: Aldolase lsrF

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.741, 107.102, 169.516
Angle α, β, γ (deg.)	90.00, 102.62, 90.00
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: 32322.145 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) / Strain (production host): K-12 References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Sugar	ChemComp-5RP / RIBULOSE-5-PHOSPHATE Type: saccharide / Mass: 230.110 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Formula: C₅H₁₁O₈P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.28 Å³/Da / Density % sol: 45.94 %
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:

SYNCHROTRON / Site:

NSLS

/ Beamline: X26C / Wavelength: 1 Å

Detector

Type: ADSC / Detector: CCD / Date: Oct 18, 2008 / Details: Si(111)

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.9→49.03 Å / Num. all: 111445 / Num. obs: 111445 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / R_merge(I) obs: 0.09 / Χ²: 1.219 / Net I/σ(I): 8.666

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.9-3	1.6	0.436	9821	1.105	1	82.1
3-3.12	1.6	0.345	10035	1.15	1	83.8
3.12-3.27	1.7	0.236	10499	1.134	1	87.6
3.27-3.44	1.6	0.17	10850	1.13	1	90.5
3.44-3.65	1.7	0.131	11276	1.364	1	94.2
3.65-3.94	1.7	0.101	11722	1.418	1	97.2
3.94-4.33	1.8	0.077	11748	1.395	1	98.4
4.33-4.96	1.8	0.063	11839	1.303	1	98.8
4.96-6.24	1.8	0.066	11850	1.232	1	98.9
6.24-50	1.8	0.038	11805	0.911	1	98.5

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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
CBASS		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3GKF

3gkf

Resolution: 2.9→49.03 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.671 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	5678	5 %	RANDOM
R_work	0.195	-	-	-
obs	0.197	107205	94.24 %	-
all	-	107205	-	-

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: 99.65 Å² / B_iso mean: 25.53 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.84 Å²	0.17 Å²	2.96 Å²
2-	-	-2.03 Å²	0.54 Å²
3-	-	-	2.48 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→49.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42260	0	280	376	42916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	43280
X-RAY DIFFRACTION	r_angle_refined_deg	1.178	1.965	58560
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.803	5	5480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.664	23.871	1860
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.905	15	7380
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.618	15	320
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	6580
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	32460
X-RAY DIFFRACTION	r_mcbond_it	0.914	1.5	27380
X-RAY DIFFRACTION	r_mcangle_it	2.087	2	44020
X-RAY DIFFRACTION	r_scbond_it	4.135	3	15900
X-RAY DIFFRACTION	r_scangle_it	7.259	4.5	14540

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2127 / 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	0.05	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	0.05	0.05
G	TIGHT POSITIONAL	0.05	0.05
H	TIGHT POSITIONAL	0.04	0.05
I	TIGHT POSITIONAL	0.04	0.05
J	TIGHT POSITIONAL	0.05	0.05
K	TIGHT POSITIONAL	0.05	0.05
L	TIGHT POSITIONAL	0.04	0.05
M	TIGHT POSITIONAL	0.05	0.05
N	TIGHT POSITIONAL	0.06	0.05
O	TIGHT POSITIONAL	0.04	0.05
P	TIGHT POSITIONAL	0.06	0.05
Q	TIGHT POSITIONAL	0.04	0.05
R	TIGHT POSITIONAL	0.04	0.05
S	TIGHT POSITIONAL	0.04	0.05
T	TIGHT POSITIONAL	0.05	0.05
A	TIGHT THERMAL	0.07	0.5
B	TIGHT THERMAL	0.09	0.5
C	TIGHT THERMAL	0.09	0.5
D	TIGHT THERMAL	0.08	0.5
E	TIGHT THERMAL	0.08	0.5
F	TIGHT THERMAL	0.08	0.5
G	TIGHT THERMAL	0.1	0.5
H	TIGHT THERMAL	0.08	0.5
I	TIGHT THERMAL	0.08	0.5
J	TIGHT THERMAL	0.1	0.5
K	TIGHT THERMAL	0.09	0.5
L	TIGHT THERMAL	0.08	0.5
M	TIGHT THERMAL	0.08	0.5
N	TIGHT THERMAL	0.1	0.5
O	TIGHT THERMAL	0.08	0.5
P	TIGHT THERMAL	0.1	0.5
Q	TIGHT THERMAL	0.07	0.5
R	TIGHT THERMAL	0.07	0.5
S	TIGHT THERMAL	0.08	0.5
T	TIGHT THERMAL	0.09	0.5

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.402	394	-
R_work	0.331	7028	-
all	-	7422	-
obs	-	-	83.71 %

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	0.3381	-0.0399	0.0039	1.0077	0.04	0.0034	0.0996	-0.2648	-0.0716	0.299	-0.1026	-0.2109	0.0113	0.0074	0.003	0.2336	-0.0861	-0.1064	0.4001	0.1423	0.0886	-0.9275	-54.2206	-6.6728
2	0.0643	0.1298	-0.0267	0.9481	-0.1426	0.0245	-0.0585	-0.0389	-0.0583	-0.1657	0.0125	-0.2351	0.0357	0.0021	0.046	0.0743	0.0261	0.0698	0.0385	0.0166	0.0765	-3.2648	-45.7205	-65.7346
3	0.2828	0.3557	-0.0196	0.5833	-0.0585	0.2158	0.025	-0.0974	0.0409	0.0276	-0.0999	0.0728	0.0481	0.07	0.0749	0.0217	0.0095	0.0132	0.0581	0.0147	0.0489	-6.978	-13.0193	-49.3163
4	0.0829	-0.0428	0.0484	0.5832	-0.2534	0.1396	0.0536	-0.1442	0.0216	0.2238	-0.0846	0.0011	-0.0562	0.0018	0.031	0.1825	-0.1053	-0.0028	0.3305	-0.0511	0.0338	-5.514	-18.188	-12.732
5	0.598	0.0765	-0.3255	0.0944	-0.0244	0.47	-0.0464	-0.1816	-0.2222	0.0332	-0.0724	-0.1421	0.0501	0.1213	0.1189	0.0794	0.0345	-0.0089	0.1066	0.145	0.2493	0.4843	-71.214	-39.3978
6	0.6665	-0.3377	-0.2655	0.3097	0.066	0.2264	0.0007	0.1928	-0.2321	-0.1032	-0.1166	0.1796	0.0534	-0.043	0.1159	0.0936	-0.0064	-0.0184	0.1008	-0.1064	0.1884	18.4472	-124.6207	-106.9822
7	0.5223	-0.2322	0.046	0.5842	-0.036	0.166	-0.0042	0.1449	0.0945	0.0064	-0.0444	-0.1525	0.0709	-0.0311	0.0486	0.0475	-0.0065	-0.0015	0.0639	-0.0024	0.0681	25.6341	-66.5201	-96.6006
8	0.1169	0.0659	-0.0646	0.685	0.078	0.1007	0.0508	0.1818	0.0234	-0.2367	-0.0638	-0.0549	-0.0179	-0.1156	0.013	0.1998	0.13	0.0303	0.3492	0.0836	0.0592	24.8751	-71.416	-133.1195
9	0.0784	-0.1801	-0.0167	0.9181	0.0011	0.0105	0.0764	0.1598	-0.0698	-0.2947	-0.0893	0.1736	0.021	-0.0532	0.013	0.2684	0.0832	-0.099	0.4741	-0.1361	0.0683	20.3182	-107.4564	-139.5891
10	0.081	-0.2467	0.0176	0.9115	-0.0244	0.0172	-0.0291	0.0115	-0.0534	0.144	0.0308	0.1868	0.0151	0.0102	-0.0016	0.045	0.0148	0.0361	0.0322	-0.0013	0.0445	21.8048	-99.3344	-80.4414
11	0.1628	0.2771	-0.0743	0.5143	-0.1792	0.101	0.0314	-0.0529	-0.0006	-0.0134	-0.0833	-0.03	0.0575	0.0299	0.052	0.0768	-0.0004	0.0383	0.0241	0.0188	0.076	47.4563	-72.9857	-46.1475
12	0.4354	-0.0324	-0.0887	0.454	-0.1752	0.2356	0.0777	-0.2694	0.0608	0.2516	-0.0454	0.1356	-0.0447	0.0122	-0.0324	0.2134	-0.0876	0.0917	0.2824	-0.1095	0.0765	42.8613	-28.0176	-7.3215
13	0.3867	0.0751	0.2619	0.3842	0.0313	0.4936	0.0115	-0.0758	0.1031	0.1021	-0.0274	0.2397	0.01	0.0691	0.0159	0.0311	-0.0018	0.0512	0.0611	-0.0475	0.1921	40.2824	-14.1332	-41.4173
14	0.0325	0.0987	-0.003	0.6228	0.2143	0.1578	-0.0212	-0.016	0.036	-0.0417	-0.0148	0.1872	0.013	0.0259	0.036	0.0293	0.0003	-0.0385	0.0155	-0.0001	0.082	43.3882	-41.737	-65.4615
15	0.2041	-0.0515	-0.1994	0.7096	0.2697	0.2807	0.032	-0.1931	-0.0799	0.3082	-0.1258	0.0938	0.0657	0.1016	0.0938	0.1917	-0.075	0.0515	0.2927	0.0897	0.0613	47.3657	-64.4679	-10.2304
16	0.2917	-0.353	0.1668	0.6636	-0.3151	0.2139	-0.0298	0.0579	0.0439	0.0664	-0.0238	-0.2028	0.0081	0.0055	0.0536	0.0333	0.0035	-0.0507	0.0239	-0.0242	0.1218	53.8865	-95.4717	-80.2117
17	0.3054	-0.0547	-0.2173	0.7369	-0.1353	0.2712	0.0325	0.2249	-0.0241	-0.3137	-0.1302	-0.1743	0.0778	-0.0924	0.0977	0.2219	0.0871	0.0933	0.333	-0.0638	0.1252	50.806	-117.7617	-135.528
18	0.3529	0.0057	0.011	0.4849	0.1993	0.215	0.1318	0.3248	0.1293	-0.2909	-0.0719	-0.2272	-0.0238	-0.0894	-0.06	0.2872	0.1225	0.1972	0.3481	0.1425	0.1685	55.3083	-81.2952	-138.1384
19	0.8728	-0.1698	0.078	0.4974	-0.0285	0.1827	0.0574	0.1006	0.2532	-0.1176	-0.0437	-0.3631	-0.0078	-0.03	-0.0137	0.0374	0.0194	0.0802	0.0235	0.0521	0.3176	57.2359	-67.6214	-103.9902
20	0.1619	-0.2858	-0.0634	0.561	0.1736	0.095	0.0189	0.0475	0.0069	0.0229	-0.0473	-0.0022	0.0501	0.0104	0.0284	0.0575	0.0285	0.022	0.0439	-0.0243	0.0878	50.0096	-126.6378	-99.7198

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 289
2	X-RAY DIFFRACTION	1	A	984
3	X-RAY DIFFRACTION	1	A	292 - 344
4	X-RAY DIFFRACTION	2	B	10 - 289
5	X-RAY DIFFRACTION	2	B	984
6	X-RAY DIFFRACTION	2	B	292 - 371
7	X-RAY DIFFRACTION	3	C	10 - 289
8	X-RAY DIFFRACTION	3	C	984
9	X-RAY DIFFRACTION	3	C	292 - 369
10	X-RAY DIFFRACTION	4	D	10 - 289
11	X-RAY DIFFRACTION	4	D	984
12	X-RAY DIFFRACTION	4	D	292 - 376
13	X-RAY DIFFRACTION	5	E	10 - 289
14	X-RAY DIFFRACTION	5	E	984
15	X-RAY DIFFRACTION	5	E	292 - 363
16	X-RAY DIFFRACTION	6	F	10 - 289
17	X-RAY DIFFRACTION	6	F	984
18	X-RAY DIFFRACTION	6	F	292 - 373
19	X-RAY DIFFRACTION	7	G	10 - 289
20	X-RAY DIFFRACTION	7	G	984
21	X-RAY DIFFRACTION	7	G	292 - 359
22	X-RAY DIFFRACTION	8	H	10 - 289
23	X-RAY DIFFRACTION	8	H	984
24	X-RAY DIFFRACTION	8	H	292 - 361
25	X-RAY DIFFRACTION	9	I	10 - 289
26	X-RAY DIFFRACTION	9	I	984
27	X-RAY DIFFRACTION	9	I	292 - 375
28	X-RAY DIFFRACTION	10	J	10 - 289
29	X-RAY DIFFRACTION	10	J	984
30	X-RAY DIFFRACTION	10	J	292 - 345
31	X-RAY DIFFRACTION	11	K	10 - 289
32	X-RAY DIFFRACTION	11	K	984
33	X-RAY DIFFRACTION	11	K	292 - 366
34	X-RAY DIFFRACTION	12	L	10 - 289
35	X-RAY DIFFRACTION	12	L	984
36	X-RAY DIFFRACTION	12	L	292 - 356
37	X-RAY DIFFRACTION	13	M	10 - 289
38	X-RAY DIFFRACTION	13	M	984
39	X-RAY DIFFRACTION	13	M	292 - 367
40	X-RAY DIFFRACTION	14	N	10 - 289
41	X-RAY DIFFRACTION	14	N	984
42	X-RAY DIFFRACTION	14	N	292 - 335
43	X-RAY DIFFRACTION	15	O	10 - 289
44	X-RAY DIFFRACTION	15	O	984
45	X-RAY DIFFRACTION	15	O	292 - 336
46	X-RAY DIFFRACTION	16	P	10 - 289
47	X-RAY DIFFRACTION	16	P	984
48	X-RAY DIFFRACTION	16	P	292 - 331
49	X-RAY DIFFRACTION	17	Q	10 - 289
50	X-RAY DIFFRACTION	17	Q	984
51	X-RAY DIFFRACTION	17	Q	292 - 365
52	X-RAY DIFFRACTION	18	R	10 - 289
53	X-RAY DIFFRACTION	18	R	984
54	X-RAY DIFFRACTION	18	R	292 - 374
55	X-RAY DIFFRACTION	19	S	10 - 289
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58	X-RAY DIFFRACTION	20	T	10 - 289
59	X-RAY DIFFRACTION	20	T	984
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