PDB-2w04: Co-complex Structure of Achromobactin Synthetase Protein D (AcsD)...

ID or keywords:

Entry

Database: PDB / ID: 2w04

Title

Co-complex Structure of Achromobactin Synthetase Protein D (AcsD) with citrate in ATP binding site from Pectobacterium Chrysanthemi

Components

ACSD

Keywords

METAL TRANSPORT / ACSD / PECTOBACTERIUM CHRYSANTHEMI / ACHROMOBACTIN BIOSYNTHESIS / 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 /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Schmelz, S. / McMahon, S.A. / Kadi, N. / Song, L. / Oves-Costales, D. / Oke, M. / Liu, H. / Johnson, K.A. / Carter, L. / White, M.F. ...

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. / Botting, C.H. / White, M.F. / Challis, G.L. / Naismith, J.H.

History

Deposition	Aug 8, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 29, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2w04.cif.gz	234.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2w04.ent.gz	189.4 KB	Display	PDB format
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Validation report

Summary document	2w04_validation.pdf.gz	462.4 KB	Display	wwPDB validaton report
Full document	2w04_full_validation.pdf.gz	480.8 KB	Display
Data in XML	2w04_validation.xml.gz	42.3 KB	Display
Data in CIF	2w04_validation.cif.gz	58.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/2w04 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w04	HTTPS FTP

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Related structure data

Related structure data	2w02C 2w03C C: citing same article (ref.)
Similar structure data	2w02-1 2w03-1 2w03-2 3fu3-d 2w02-2 5fh4-d 3moe-d 2rk8-1 2rka-1 3chp-d 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: ACSD

B: ACSD

hetero molecules

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

1

A: ACSD

defined by author&software
70.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ACSD

hetero molecules

defined by author&software
70.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.371, 94.959, 160.261
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:
NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-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	SER	SER	GLY	GLY	A	A	14 - 35	14 - 35
2	1	SER	SER	GLY	GLY	B	B	14 - 35	14 - 35
1	2	TYR	TYR	VAL	VAL	A	A	36 - 78	36 - 78
2	2	TYR	TYR	VAL	VAL	B	B	36 - 78	36 - 78
1	3	ASP	ASP	ALA	ALA	A	A	79 - 154	79 - 154
2	3	ASP	ASP	ALA	ALA	B	B	79 - 154	79 - 154
1	4	PRO	PRO	LYS	LYS	A	A	155 - 177	155 - 177
2	4	PRO	PRO	LYS	LYS	B	B	155 - 177	155 - 177
1	5	ALA	ALA	ALA	ALA	A	A	178 - 199	178 - 199
2	5	ALA	ALA	ALA	ALA	B	B	178 - 199	178 - 199
1	6	LEU	LEU	VAL	VAL	A	A	200 - 273	200 - 273
2	6	LEU	LEU	VAL	VAL	B	B	200 - 273	200 - 273
1	7	ALA	ALA	PRO	PRO	A	A	274 - 342	274 - 342
2	7	ALA	ALA	PRO	PRO	B	B	274 - 342	274 - 342
1	8	GLY	GLY	THR	THR	A	A	343 - 386	343 - 386
2	8	GLY	GLY	THR	THR	B	B	343 - 386	343 - 386
1	9	LEU	LEU	ASP	ASP	A	A	387 - 421	387 - 421
2	9	LEU	LEU	ASP	ASP	B	B	387 - 421	387 - 421
1	10	TYR	TYR	GLN	GLN	A	A	422 - 446	422 - 446
2	10	TYR	TYR	GLN	GLN	B	B	422 - 446	422 - 446
1	11	ASN	ASN	GLU	GLU	A	A	447 - 466	447 - 466
2	11	ASN	ASN	GLU	GLU	B	B	447 - 466	447 - 466
1	12	GLY	GLY	CYS	CYS	A	A	467 - 505	467 - 505
2	12	GLY	GLY	CYS	CYS	B	B	467 - 505	467 - 505
1	13	LEU	LEU	ILE	ILE	A	A	506 - 515	506 - 515
2	13	LEU	LEU	ILE	ILE	B	B	506 - 515	506 - 515
1	14	LEU	LEU	TRP	TRP	A	A	516 - 530	516 - 530
2	14	LEU	LEU	TRP	TRP	B	B	516 - 530	516 - 530
1	15	ARG	ARG	ALA	ALA	A	A	531 - 539	531 - 539
2	15	ARG	ARG	ALA	ALA	B	B	531 - 539	531 - 539
1	16	ILE	ILE	GLY	GLY	A	A	540 - 557	540 - 557
2	16	ILE	ILE	GLY	GLY	B	B	540 - 557	540 - 557
1	17	HIS	HIS	LEU	LEU	A	A	558 - 570	558 - 570
2	17	HIS	HIS	LEU	LEU	B	B	558 - 570	558 - 570

NCS ensembles :

#1: Protein	ACSD Mass: 70598.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q93AT8
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE FIRST 5 RESIDUES IN CHAIN A (MNNRN) AND 6 RESIDUES IN CHAIN B (MNNRNH) ARE DISORDERED. RESIDUES ...THE FIRST 5 RESIDUES IN CHAIN A (MNNRN) AND 6 RESIDUES IN CHAIN B (MNNRNH) ARE DISORDERED. RESIDUES 99 (Q) AND 572- 577 (AEADRQ) IN CHAIN A ARE DISORDERED. IN CHAIN B RESIDUES 98-99 (AQ) AND 573-576 (EADR) ARE DISORDERED. IN BOTH CHAINS RESIDUE 588-620 ( GHAVQHGSEVQHDERRHGDVRHEEARHGEVQHG) ARE DISORDERED.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 43 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 7.8 Details: 26%PEG8000, 0.1M TRIS-HCL PH7.8, 300MM SODIUM CITRATE ACSD WAS INCUBATED WITH 2 MM ATP-GAMMA-S (SIGMA A1388) FOR 10 MIN (RT). 3UL ACSD (6MG/ML) AND EQUAL AMOUNT OF PRECIPITANT WERE INCUBATED ...Details: 26%PEG8000, 0.1M TRIS-HCL PH7.8, 300MM SODIUM CITRATE ACSD WAS INCUBATED WITH 2 MM ATP-GAMMA-S (SIGMA A1388) FOR 10 MIN (RT). 3UL ACSD (6MG/ML) AND EQUAL AMOUNT OF PRECIPITANT WERE INCUBATED IN CONVENTIONAL HANGING DROP PLATES.

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 43 % / Description: NONE

Crystal grow

Method: vapor diffusion, hanging drop / pH: 7.8
Details: 26%PEG8000, 0.1M TRIS-HCL PH7.8, 300MM SODIUM CITRATE ACSD WAS INCUBATED WITH 2 MM ATP-GAMMA-S (SIGMA A1388) FOR 10 MIN (RT). 3UL ACSD (6MG/ML) AND EQUAL AMOUNT OF PRECIPITANT WERE INCUBATED ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9803
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2007 / Details: SINGLE SILICON (111) MONOCHROMATOR
Radiation	Monochromator: SINGLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9803 Å / Relative weight: 1
Reflection	Resolution: 2.8→81.6 Å / Num. obs: 30736 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / R_merge(I) obs: 0.16 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: APO STRUCTURE OF ACSD

Resolution: 2.8→81.65 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.832 / SU B: 35.931 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28	1513	4.9 %	RANDOM
R_work	0.202	-	-	-
obs	0.206	29085	98.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 11.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.53 Å²	0 Å²	0 Å²
2-	-	-1.78 Å²	0 Å²
3-	-	-	3.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→81.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9215	0	13	130	9358

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	9468
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.461	1.947	12867
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.4	5	1144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.559	23.395	483
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.007	15	1538
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.691	15	85
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1369
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7403
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	4736
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	6379
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	381
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	0.252	0.2	79
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.252	0.2	11
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	0.451	1.5	5881
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.783	2	9214
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.096	3	4079
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.823	4.5	3653
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	88	tight positional	0.04	0.05
1	2	B	88	tight positional	0.04	0.05
2	1	A	172	tight positional	0.06	0.05
2	2	B	172	tight positional	0.06	0.05
3	1	A	292	tight positional	0.06	0.05
3	2	B	292	tight positional	0.06	0.05
4	1	A	92	tight positional	0.06	0.05
4	2	B	92	tight positional	0.06	0.05
5	1	A	88	tight positional	0.11	0.05
5	2	B	88	tight positional	0.11	0.05
6	1	A	296	tight positional	0.05	0.05
6	2	B	296	tight positional	0.05	0.05
7	1	A	276	tight positional	0.07	0.05
7	2	B	276	tight positional	0.07	0.05
8	1	A	176	tight positional	0.07	0.05
8	2	B	176	tight positional	0.07	0.05
9	1	A	140	tight positional	0.06	0.05
9	2	B	140	tight positional	0.06	0.05
10	1	A	100	tight positional	0.05	0.05
10	2	B	100	tight positional	0.05	0.05
11	1	A	80	tight positional	0.05	0.05
11	2	B	80	tight positional	0.05	0.05
12	1	A	156	tight positional	0.05	0.05
12	2	B	156	tight positional	0.05	0.05
13	1	A	40	tight positional	0.04	0.05
13	2	B	40	tight positional	0.04	0.05
14	1	A	60	tight positional	0.04	0.05
14	2	B	60	tight positional	0.04	0.05
15	1	A	36	tight positional	0.05	0.05
15	2	B	36	tight positional	0.05	0.05
16	1	A	72	tight positional	0.06	0.05
16	2	B	72	tight positional	0.06	0.05
17	1	A	52	tight positional	0.04	0.05
17	2	B	52	tight positional	0.04	0.05
1	1	A	76	medium positional	0.32	0.5
1	2	B	76	medium positional	0.32	0.5
2	1	A	178	medium positional	0.47	0.5
2	2	B	178	medium positional	0.47	0.5
3	1	A	296	medium positional	0.58	0.5
3	2	B	296	medium positional	0.58	0.5
4	1	A	97	medium positional	0.39	0.5
4	2	B	97	medium positional	0.39	0.5
5	1	A	92	medium positional	0.61	0.5
5	2	B	92	medium positional	0.61	0.5
6	1	A	272	medium positional	0.44	0.5
6	2	B	272	medium positional	0.44	0.5
7	1	A	277	medium positional	0.61	0.5
7	2	B	277	medium positional	0.61	0.5
8	1	A	161	medium positional	0.51	0.5
8	2	B	161	medium positional	0.51	0.5
9	1	A	153	medium positional	0.56	0.5
9	2	B	153	medium positional	0.56	0.5
10	1	A	111	medium positional	0.32	0.5
10	2	B	111	medium positional	0.32	0.5
11	1	A	86	medium positional	0.48	0.5
11	2	B	86	medium positional	0.48	0.5
12	1	A	173	medium positional	0.64	0.5
12	2	B	173	medium positional	0.64	0.5
13	1	A	43	medium positional	0.16	0.5
13	2	B	43	medium positional	0.16	0.5
14	1	A	57	medium positional	0.38	0.5
14	2	B	57	medium positional	0.38	0.5
15	1	A	44	medium positional	0.91	0.5
15	2	B	44	medium positional	0.91	0.5
16	1	A	59	medium positional	0.52	0.5
16	2	B	59	medium positional	0.52	0.5
17	1	A	50	medium positional	0.62	0.5
17	2	B	50	medium positional	0.62	0.5
1	1	A	88	tight thermal	0.08	0.5
1	2	B	88	tight thermal	0.08	0.5
2	1	A	172	tight thermal	0.1	0.5
2	2	B	172	tight thermal	0.1	0.5
3	1	A	292	tight thermal	0.1	0.5
3	2	B	292	tight thermal	0.1	0.5
4	1	A	92	tight thermal	0.09	0.5
4	2	B	92	tight thermal	0.09	0.5
5	1	A	88	tight thermal	0.11	0.5
5	2	B	88	tight thermal	0.11	0.5
6	1	A	296	tight thermal	0.1	0.5
6	2	B	296	tight thermal	0.1	0.5
7	1	A	276	tight thermal	0.08	0.5
7	2	B	276	tight thermal	0.08	0.5
8	1	A	176	tight thermal	0.08	0.5
8	2	B	176	tight thermal	0.08	0.5
9	1	A	140	tight thermal	0.08	0.5
9	2	B	140	tight thermal	0.08	0.5
10	1	A	100	tight thermal	0.09	0.5
10	2	B	100	tight thermal	0.09	0.5
11	1	A	80	tight thermal	0.06	0.5
11	2	B	80	tight thermal	0.06	0.5
12	1	A	156	tight thermal	0.06	0.5
12	2	B	156	tight thermal	0.06	0.5
13	1	A	40	tight thermal	0.08	0.5
13	2	B	40	tight thermal	0.08	0.5
14	1	A	60	tight thermal	0.09	0.5
14	2	B	60	tight thermal	0.09	0.5
15	1	A	36	tight thermal	0.08	0.5
15	2	B	36	tight thermal	0.08	0.5
16	1	A	72	tight thermal	0.09	0.5
16	2	B	72	tight thermal	0.09	0.5
17	1	A	52	tight thermal	0.08	0.5
17	2	B	52	tight thermal	0.08	0.5
1	1	A	76	medium thermal	0.64	2
1	2	B	76	medium thermal	0.64	2
2	1	A	178	medium thermal	0.65	2
2	2	B	178	medium thermal	0.65	2
3	1	A	296	medium thermal	0.63	2
3	2	B	296	medium thermal	0.63	2
4	1	A	97	medium thermal	0.58	2
4	2	B	97	medium thermal	0.58	2
5	1	A	92	medium thermal	0.58	2
5	2	B	92	medium thermal	0.58	2
6	1	A	272	medium thermal	0.58	2
6	2	B	272	medium thermal	0.58	2
7	1	A	277	medium thermal	0.51	2
7	2	B	277	medium thermal	0.51	2
8	1	A	161	medium thermal	0.56	2
8	2	B	161	medium thermal	0.56	2
9	1	A	153	medium thermal	0.58	2
9	2	B	153	medium thermal	0.58	2
10	1	A	111	medium thermal	0.65	2
10	2	B	111	medium thermal	0.65	2
11	1	A	86	medium thermal	0.72	2
11	2	B	86	medium thermal	0.72	2
12	1	A	173	medium thermal	0.44	2
12	2	B	173	medium thermal	0.44	2
13	1	A	43	medium thermal	0.49	2
13	2	B	43	medium thermal	0.49	2
14	1	A	57	medium thermal	0.52	2
14	2	B	57	medium thermal	0.52	2
15	1	A	44	medium thermal	0.95	2
15	2	B	44	medium thermal	0.95	2
16	1	A	59	medium thermal	0.54	2
16	2	B	59	medium thermal	0.54	2
17	1	A	50	medium thermal	0.67	2
17	2	B	50	medium thermal	0.67	2

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.417	88
R_work	0.266	2150

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