PDB-1qya: CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE

ID or keywords:

Entry

Database: PDB / ID: 1qya

Title

CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE

Components

HYPOTHETICAL PROTEIN yddE

Keywords

UNKNOWN FUNCTION / PUTATIVE PHENAZINE BIOSYNTHESIS PROTEIN / EPIMERASE / ANTIBIOTIC BIOSYNTHESIS PROTEIN / STRUCTURAL GENOMICS

Function / homology

Function and homology information

Isomerases; Racemases and epimerases / isomerase activity / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Grassick, A. / Sulzenbacher, G. / Roig-Zamboni, V. / Campanacci, V. / Cambillau, C. / Bourne, Y.

Citation

Journal: Proteins / Year: 2004
Title: Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase
Authors: Grassick, A. / Sulzenbacher, G. / Roig-Zamboni, V. / Campanacci, V. / Cambillau, C. / Bourne, Y.

History

Deposition	Sep 10, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1qya.cif.gz	134.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1qya.ent.gz	105.8 KB	Display	PDB format
PDBx/mmJSON format	1qya.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/1qya ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qya	HTTPS FTP

-
Related structure data

Related structure data	1qy9C C: citing same article (ref.)
Similar structure data	7a9x-d 2fue-1 4rld-5 1qy9-2 4uzd-d 3tej-d 2clp-3 5ha4-d 1uwx-2 1qy9-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HYPOTHETICAL PROTEIN yddE

B: HYPOTHETICAL PROTEIN yddE

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.159, 79.631, 77.022
Angle α, β, γ (deg.)	90.00, 115.26, 90.00
Int Tables number	4
Cell setting	monoclinic
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	VAL	VAL	5	A	A	4 - 24	14 - 34
2	1	GLN	GLN	VAL	VAL	5	B	B	4 - 24	14 - 34
3	2	ALA	ALA	GLN	GLN	6	A	A	33 - 36	43 - 46
4	2	ALA	ALA	GLN	GLN	6	B	B	33 - 36	43 - 46
5	3	LEU	LEU	GLU	GLU	5	A	A	37 - 41	47 - 51
6	3	LEU	LEU	GLU	GLU	5	B	B	37 - 41	47 - 51
7	4	LEU	LEU	GLU	GLU	6	A	A	42 - 46	52 - 56
8	4	LEU	LEU	GLU	GLU	6	B	B	42 - 46	52 - 56
9	5	THR	THR	PHE	PHE	5	A	A	47 - 49	57 - 59
10	5	THR	THR	PHE	PHE	5	B	B	47 - 49	57 - 59
11	6	TYR	TYR	THR	THR	5	A	A	62 - 66	72 - 76
12	6	TYR	TYR	THR	THR	5	B	B	62 - 66	72 - 76
13	7	ALA	ALA	ALA	ALA	5	A	A	75 - 84	85 - 94
14	7	ALA	ALA	ALA	ALA	5	B	B	75 - 84	85 - 94
15	8	LYS	LYS	GLN	GLN	6	A	A	85 - 96	95 - 106
16	8	LYS	LYS	GLN	GLN	6	B	B	85 - 96	95 - 106
17	9	THR	THR	TYR	TYR	6	A	A	106 - 114	116 - 124
18	9	THR	THR	TYR	TYR	6	B	B	106 - 114	116 - 124
19	10	ARG	ARG	LEU	LEU	6	A	A	115 - 118	125 - 128
20	10	ARG	ARG	LEU	LEU	6	B	B	115 - 118	125 - 128
21	11	GLU	GLU	ASP	ASP	5	A	A	119 - 147	129 - 157
22	11	GLU	GLU	ASP	ASP	5	B	B	119 - 147	129 - 157
23	12	ILE	ILE	THR	THR	5	A	A	148 - 159	158 - 169
24	12	ILE	ILE	THR	THR	5	B	B	148 - 159	158 - 169
25	13	GLY	GLY	VAL	VAL	6	A	A	160 - 164	170 - 174
26	13	GLY	GLY	VAL	VAL	6	B	B	160 - 164	170 - 174
27	14	MET	MET	ILE	ILE	4	A	A	165 - 187	175 - 197
28	14	MET	MET	ILE	ILE	4	B	B	165 - 187	175 - 197
29	15	SER	SER	ASN	ASN	6	A	A	188 - 194	198 - 204
30	15	SER	SER	ASN	ASN	6	B	B	188 - 194	198 - 204
31	16	GLY	GLY	GLY	GLY	5	A	A	195 - 204	205 - 214
32	16	GLY	GLY	GLY	GLY	5	B	B	195 - 204	205 - 214
33	17	LYS	LYS	VAL	VAL	5	A	A	205 - 220	215 - 230
34	17	LYS	LYS	VAL	VAL	5	B	B	205 - 220	215 - 230
35	18	GLU	GLU	LEU	LEU	5	A	A	221 - 236	231 - 246
36	18	GLU	GLU	LEU	LEU	5	B	B	221 - 236	231 - 246
37	19	ASN	ASN	VAL	VAL	6	A	A	240 - 248	250 - 258
38	19	ASN	ASN	VAL	VAL	6	B	B	240 - 248	250 - 258
39	20	LEU	LEU	VAL	VAL	5	A	A	249 - 286	259 - 296
40	20	LEU	LEU	VAL	VAL	5	B	B	249 - 286	259 - 296

#1: Protein	HYPOTHETICAL PROTEIN yddE / ORFB Mass: 33406.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDDE / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P37757
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 600, 0.1 M IMIDAZOLE-MALATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-1 / Wavelength: 0.9330,0.9340

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2002

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.933	1
2	0.934	1

Reflection

Resolution: 2→20 Å / Num. obs: 49349 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.044 / Net I/σ(I): 12

Reflection shell

Resolution: 2→2.05 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.431 / Mean I/σ(I) obs: 1.7 / % possible all: 94.6

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALA		data scaling
MOLREP		phasing
REFMAC	5.1.19	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: YDDE SOLVED BY SAD ON SE-MET EDGE

Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.948 / SU B: 4.419 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22761	2407	5.2 %	RANDOM
R_work	0.18626	-	-	-
obs	0.18838	44289	94.07 %	-

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_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	-1.69 Å²
2-	-	1.21 Å²	0 Å²
3-	-	-	-2.94 Å²

Refinement step

Cycle: LAST / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4610	0	0	270	4880

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	4766
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4340
X-RAY DIFFRACTION	r_angle_refined_deg	1.201	1.945	6499
X-RAY DIFFRACTION	r_angle_other_deg	0.767	3	10119
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.117	5	612
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	741
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5347
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	911
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	777
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	4843
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	2903
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	223
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.082	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.271	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.058	0.2	8
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.52	1.5	3014
X-RAY DIFFRACTION	r_mcangle_it	0.953	2	4893
X-RAY DIFFRACTION	r_scbond_it	1.457	3	1752
X-RAY DIFFRACTION	r_scangle_it	2.453	4.5	1599
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
2750	medium positional	0.33	0.5
790	loose positional	0.7	5
2750	medium thermal	0.4	2
790	loose thermal	1.47	10

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.311	159
R_work	0.284	3007

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	2.8043	-0.6076	1.6401	3.9158	-1.0281	7.3617	0.3105	0.0337	-0.3604	-0.5243	0.0079	0.3499	1.2172	-0.3426	-0.3183	0.2827	-0.0287	-0.0411	0.1351	0.0214	0.2223	49.3925	-1.8132	19.8612
2	2.3963	-1.3084	0.8247	6.0914	-7.149	6.4586	0.0673	-0.11	-0.286	-0.5247	-0.1465	0.0464	0.8566	0.1749	0.0791	0.2639	-0.0515	-0.0334	0.1879	0.0085	0.2289	52.6608	-7.0501	29.7446
3	32.1632	-9.2218	-11.4322	4.5664	2.9441	7.4138	0.156	-0.508	-0.0448	-0.1438	0.2043	0.1421	-0.3611	-0.1274	-0.3603	0.1566	-0.0892	-0.0111	0.0888	0.0369	0.1411	59.159	-5.4597	34.5628
4	2.1946	-0.4655	-0.179	4.5568	0.4283	2.6172	0.0461	0.096	0.4268	-0.1808	0.01	-0.4002	-0.2331	0.3988	-0.0562	0.0561	-0.0863	0.0349	0.1542	-0.0306	0.272	81.427	4.9452	24.0259
5	2.6169	-0.863	0.2969	3.1372	-1.2307	2.5288	-0.0386	-0.1556	0.112	0.1272	0.0515	0.0374	-0.0769	0.0437	-0.013	0.0638	-0.0581	0.0085	0.0857	-0.0684	0.1723	71.1632	1.2895	33.1886
6	7.9775	-1.6801	6.697	1.9207	-3.0592	8.791	0.2536	0.3064	-0.3806	-0.5208	0.2297	0.2737	0.8348	-0.2762	-0.4833	0.1879	-0.068	0.0181	0.2246	0.0336	0.1979	43.1879	4.0582	21.7259
7	10.284	-11.1414	-2.3146	12.9085	0.0364	8.2984	-0.0887	0.0001	-0.4806	0.2252	0.1207	0.7041	0.3648	-0.9587	-0.032	0.11	-0.0512	0.0203	0.2863	-0.0134	0.1923	27.752	22.9271	21.0063
8	2.0266	-0.3227	0.4109	2.1009	-0.2222	2.7428	-0.017	-0.1379	0.1186	-0.0455	0.0516	-0.069	-0.1172	-0.069	-0.0346	0.0963	-0.0116	0.043	0.1359	0.0178	0.138	44.011	19.9825	16.4188
9	5.4069	-0.3513	1.2233	2.1464	-0.6143	2.6183	-0.0085	0.6335	0.396	-0.3761	0.0037	0.0538	-0.2635	-0.2163	0.0048	0.1901	0.0397	0.029	0.2494	0.0118	0.1705	37.4767	24.9196	8.2428
10	24.8367	18.2297	-14.5988	15.3501	-12.9793	12.7615	-0.144	-0.0694	0.0994	-0.4292	0.2751	0.3179	0.1648	-0.5143	-0.1311	0.1748	0.0435	-0.0099	0.2373	-0.0246	0.125	37.8685	24.303	-0.2454
11	2.9597	0.1253	0.4158	6.8466	-0.6713	3.2583	-0.0136	0.1658	-0.1863	-0.1626	-0.2706	-0.9512	0.2876	0.6931	0.2842	0.1191	0.0422	0.0422	0.277	0.0747	0.2663	61.2233	19.9222	-12.8457
12	2.8562	-0.3545	-0.4835	4.4097	-2.089	3.2838	-0.0371	0.0469	0.0185	0.1744	-0.0416	0.0513	0.1686	-0.1362	0.0787	0.1372	-0.0294	0.0041	0.1678	-0.045	0.0761	47.288	20.446	-9.4739
13	2.7683	-1.1824	1.8716	1.9017	-1.9433	8.4013	-0.0122	-0.3999	-0.0162	0.0683	0.1315	-0.0177	-0.0487	-0.3289	-0.1193	0.0645	-0.0448	0.0273	0.2083	0.0218	0.173	40.4791	12.4469	19.1274

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	1 - 65	11 - 75
2	X-RAY DIFFRACTION	2	A	A	66 - 111	76 - 121
3	X-RAY DIFFRACTION	3	A	A	112 - 124	122 - 134
4	X-RAY DIFFRACTION	4	A	A	125 - 192	135 - 202
5	X-RAY DIFFRACTION	5	A	A	193 - 282	203 - 292
6	X-RAY DIFFRACTION	6	A	A	283 - 297	293 - 307
7	X-RAY DIFFRACTION	7	B	B	-8 - 0	2 - 10
8	X-RAY DIFFRACTION	8	B	B	1 - 65	11 - 75
9	X-RAY DIFFRACTION	9	B	B	66 - 111	76 - 121
10	X-RAY DIFFRACTION	10	B	B	112 - 124	122 - 134
11	X-RAY DIFFRACTION	11	B	B	125 - 192	135 - 202
12	X-RAY DIFFRACTION	12	B	B	193 - 282	203 - 292
13	X-RAY DIFFRACTION	13	B	B	283 - 297	293 - 307

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi