PDB-3ffe: Structure of Achromobactin Synthetase Protein D, (AcsD)

ID or keywords:

Entry

Database: PDB / ID: 3ffe

Title

Structure of Achromobactin Synthetase Protein D, (AcsD)

Components

AcsD

Keywords

BIOSYNTHETIC PROTEIN / Acsd / adenylating enzyme /

siderophore /

Structural Genomics / Scottish Structural Proteomics Facility / SSPF

Function / homology

Function and homology information

acid-amino acid ligase activity / siderophore biosynthetic process /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

Erwinia chrysanthemi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

McMahon, S.A. / Liu, H. / Carter, L. / Oke, M. / Johnson, K.A. / Schmelz, S. / Challis, G.L. / White, M.F. / Naismith, J.H. / Scottish Structural Proteomics Facility (SSPF)

Citation

Journal: Nat.Chem.Biol. / Year: 2009
Title: AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis
Authors: Schmelz, S. / Kadi, N. / McMahon, S.A. / Song, L. / Oves-Costales, D. / Oke, M. / Liu, H. / Johnson, K.A. / Carter, L.G. / Botting, C.H. / White, M.F. / Challis, G.L. / Naismith, J.H.

History

Deposition	Dec 3, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Dec 27, 2023	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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ffe.cif.gz	248.8 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	2w02 2w03 2w04
Similar structure data	2w02-d 2w04-d 2x3j-d 2x3k-d 2w03-d 3lem-2 3q0z-3 3lih-2 1fm6-d 3ldk-2 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

Deposited unit

A: AcsD

B: AcsD

149 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)	80.328, 95.729, 160.520
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	MET	MET	A	A	7 - 65	40 - 98
2	1	ASP	ASP	MET	MET	B	B	7 - 65	40 - 98
1	2	VAL	VAL	HIS	HIS	A	A	76 - 120	109 - 153
2	2	VAL	VAL	HIS	HIS	B	B	76 - 120	109 - 153
1	3	GLU	GLU	ARG	ARG	A	A	128 - 179	161 - 212
2	3	GLU	GLU	ARG	ARG	B	B	128 - 179	161 - 212
1	4	GLU	GLU	ASN	ASN	A	A	188 - 297	221 - 330
2	4	GLU	GLU	ASN	ASN	B	B	188 - 297	221 - 330
1	5	TRP	TRP	THR	THR	A	A	309 - 400	342 - 433
2	5	TRP	TRP	THR	THR	B	B	309 - 400	342 - 433
1	6	GLY	GLY	GLY	GLY	A	A	407 - 475	440 - 508
2	6	GLY	GLY	GLY	GLY	B	B	407 - 475	440 - 508
1	7	PRO	PRO	VAL	VAL	A	A	485 - 581	518 - 614
2	7	PRO	PRO	VAL	VAL	B	B	485 - 581	518 - 614

#1: Protein	AcsD Mass: 74389.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Gene: acsD / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93AT8
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.07 Å³/Da / Density % sol: 40.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, pH8.5, 1.0M sodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	BM14	1	0.976
SYNCHROTRON	ESRF	ID14-4	2	0.979

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 225 mm CCD	1	CCD	Sep 12, 2006	mirrors
ADSC QUANTUM 315	2	CCD	Jul 25, 2006	torodial focusing mirror

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.976	1
2	0.979	1

Reflection

Resolution: 2.25→50 Å / Num. obs: 56200 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / R_merge(I) obs: 0.098 / Net I/σ(I): 11.5

Reflection shell

Resolution: 2.25→2.38 Å / Redundancy: 3 % / R_merge(I) obs: 0.402 / Mean I/σ(I) obs: 3.2 / % possible all: 91.5

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Processing

Software

Name	Version	Classification
XDS		data scaling
SHELXS		phasing
REFMAC	5.2.0019	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.25→28.72 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.908 / SU B: 13.063 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24055	2970	5.1 %	RANDOM
R_work	0.18634	-	-	-
obs	0.18907	55464	98.25 %	-

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 mean: 18.294 Å²

	B_aniso -1	B_aniso -2
1-	-0.05 Å²	0 Å²
2-	-	0.06 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.25→28.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9205	0	0	501	9706

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	9500
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6516
X-RAY DIFFRACTION	r_angle_refined_deg	1.093	1.946	12920
X-RAY DIFFRACTION	r_angle_other_deg	0.843	3	15751
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.876	5	1156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.046	23.395	486
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.661	15	1546
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.045	15	86
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1376
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10689
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2005
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1971
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	6791
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	4540
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	4926
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	428
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.02	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.267	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.285	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	0.673	1.5	7482
X-RAY DIFFRACTION	r_mcbond_other	0.089	1.5	2316
X-RAY DIFFRACTION	r_mcangle_it	0.728	2	9262
X-RAY DIFFRACTION	r_scbond_it	1.217	3	4349
X-RAY DIFFRACTION	r_scangle_it	1.856	4.5	3655

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6941 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
loose positional	0.61	5
loose thermal	1.61	10

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	210	-
R_work	0.238	4115	-
obs	-	-	99.65 %

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	0.6577	-0.2932	-0.0715	1.6638	-0.3589	1.2311	0.0622	-0.053	0.0171	0.0427	-0.1217	-0.2015	-0.0666	0.2187	0.0595	-0.0158	-0.0396	0.0479	0.0494	0.0255	0.0138	71.701	25.559	111.928
2	0.6837	1.1262	-0.2049	3.5288	0.1825	1.5478	0.1031	0.0698	-0.0795	-0.1091	-0.0886	-0.2375	0.1345	0.1671	-0.0145	0.0591	0.0382	0.0874	-0.0114	0.0178	-0.0242	65.282	4.087	106.625
3	1.7055	-0.0702	-0.8109	1.359	-0.0364	1.6568	-0.006	-0.0014	-0.0838	0.0344	0.0056	0.0137	0.0702	-0.0033	0.0004	0.0223	-0.009	0.0373	-0.009	0.0015	-0.0262	56.58	-20.069	111.809
4	3.4802	-1.9937	-2.1368	1.1422	1.2242	1.312	1.1353	-0.243	0.9357	1.3399	-0.4413	0.0714	-0.868	0.3495	-0.694	0.2655	-0.1234	0.0424	0.1938	-0.0195	0.1495	64.847	-8.67	120.92
5	0.3753	-0.279	-0.2466	1.3548	0.2331	0.3526	0.0531	0.0263	-0.0124	0.0598	-0.0873	0.1613	-0.0064	-0.0193	0.0342	0.0103	-0.0085	0.047	0.0174	-0.0209	-0.0022	47.904	1.296	119.175
6	1.0173	0.1206	-0.0197	1.3623	-0.2526	1.4071	0.0471	-0.0438	-0.0066	0.0705	-0.0482	0.0335	0.0696	-0.003	0.0012	-0.0179	0.0051	0.0531	-0.005	-0.0322	-0.006	50.582	9.242	127.66
7	12.1369	0.0761	-10.5953	6.2785	1.2909	9.543	-0.4131	-0.457	-1.2215	0.2463	-0.0759	0.1653	0.724	0.262	0.4889	-0.0184	-0.0591	-0.0988	0.0286	-0.0162	-0.0357	66.246	14.318	126.553
8	1.2059	0.5822	-0.1064	2.5013	-0.632	0.9617	-0.0441	0.0099	-0.1256	-0.2628	-0.0963	-0.2391	0.1973	0.2419	0.1404	0.0552	0.0644	0.0764	-0.0061	0.047	0.0173	70.599	34.407	87.876
9	0.4837	-0.2156	0.0318	2.4756	0.2318	0.4381	0.085	-0.102	-0.0416	-0.0505	-0.0544	-0.4703	-0.0507	0.0905	-0.0306	0.0044	-0.0218	0.0226	0.0416	0.0685	0.0577	68.82	52.491	93.12
10	1.7709	0.6431	-0.0223	2.0439	-0.5841	1.4493	0.035	-0.0685	0.0964	0.1379	-0.0191	0.0645	-0.0507	-0.0151	-0.0159	0.0045	-0.0071	0.0368	0.0021	-0.0031	-0.0329	58.097	79.587	88.956
11	5.2655	3.3264	0.9252	2.3938	1.5351	3.2534	0.484	-0.3304	-0.9315	0.4694	-0.1603	-0.3176	0.7055	0.6829	-0.3237	0.1605	0.0342	-0.0249	0.1927	0.012	0.2014	64.806	69.402	78.704
12	0.7566	0.1479	0.192	0.9407	-0.0824	0.7603	0.0223	0.0223	-0.0325	-0.1499	0.0075	0.1172	0.1131	-0.0593	-0.0298	-0.0192	0.0348	0.0115	0.018	-0.0118	-0.0099	49.151	59.392	79.637
13	1.0126	-0.1388	0.071	1.6507	-0.5014	0.9884	-0.0663	0.0786	-0.1225	-0.201	0.0278	0.0142	0.1321	0.0009	0.0385	0.0173	-0.0084	-0.0108	0.0016	-0.0152	-0.0208	52.828	53.903	72.561
14	15.8758	4.5524	6.7926	3.195	0.8262	7.9135	-0.9034	0.5591	0.8818	-0.6805	0.2743	0.481	-0.0871	-0.241	0.6291	0.119	0.0309	0.0685	-0.0064	0.0314	0.0197	60.906	47.419	67.591

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 120
2	X-RAY DIFFRACTION	2	A	121 - 193
3	X-RAY DIFFRACTION	3	A	194 - 293
4	X-RAY DIFFRACTION	4	A	294 - 312
5	X-RAY DIFFRACTION	5	A	313 - 440
6	X-RAY DIFFRACTION	6	A	441 - 562
7	X-RAY DIFFRACTION	7	A	563 - 587
8	X-RAY DIFFRACTION	8	B	7 - 120
9	X-RAY DIFFRACTION	9	B	121 - 193
10	X-RAY DIFFRACTION	10	B	194 - 293
11	X-RAY DIFFRACTION	11	B	294 - 312
12	X-RAY DIFFRACTION	12	B	313 - 440
13	X-RAY DIFFRACTION	13	B	441 - 562
14	X-RAY DIFFRACTION	14	B	563 - 587

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