PDB-3dci: The Structure of a putative arylesterase from Agrobacterium tumef...

ID or keywords:

Entry

Database: PDB / ID: 3dci

Title

The Structure of a putative arylesterase from Agrobacterium tumefaciens str. C58

Components

Arylesterase

Keywords

HYDROLASE / Agrobacterium tumefaciens / arylesterase / SGNH_hydrolase subfamily / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function

Biological species

Agrobacterium tumefaciens str. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Cuff, M.E. / Xu, X. / Zheng, H. / Binkowski, T.A. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of a putative arylesterase from Agrobacterium tumefaciens str. C58
Authors: Cuff, M.E. / Xu, X. / Zheng, H. / Binkowski, T.A. / Edwards, A. / Savchenko, A. / Joachimiak, A.

History

Deposition	Jun 3, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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	3dci.cif.gz	142 KB	Display	PDBx/mmCIF format
PDB format	pdb3dci.ent.gz	109.6 KB	Display	PDB format
PDBx/mmJSON format	3dci.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3dci_validation.pdf.gz	455 KB	Display	wwPDB validaton report
Full document	3dci_full_validation.pdf.gz	455.6 KB	Display
Data in XML	3dci_validation.xml.gz	33.3 KB	Display
Data in CIF	3dci_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/3dci ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dci	HTTPS FTP

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Related structure data

Similar structure data	4tx1-1 7bxc-2 7bxb-d 7bxc-1 3iwt-1 7bxc-3 2j5g-1 2r86-2 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
Other databases	TargetDB: apc7346

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Arylesterase

B: Arylesterase

C: Arylesterase

hetero molecules

75.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Arylesterase

B: Arylesterase

C: Arylesterase

hetero molecules

A: Arylesterase

B: Arylesterase

C: Arylesterase

hetero molecules

defined by author&software
151 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.204, 131.397, 122.332
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-214- CL
2	1	A-235- HOH
3	1	B-357- HOH

Details

authors state that the biological assembly is unknown but may be a hexamer. The contents of the AU: x,y,z, plus that of the neighboring AU: -x+1,y,-z+1/2.

#1: Protein	Arylesterase Mass: 24833.402 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: AGR_L_2749, Atu3454 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A9CF87
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate pH 4.6, 3.2M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97921, 0.97941

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Nov 21, 2006

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97921	1
2	0.97941	1

Reflection

Redundancy: 7.4 % / Av σ(I) over netI: 6.5 / Number: 305360 / R_merge(I) obs: 0.088 / Χ²: 1.08 / D res high: 2 Å / D res low: 50 Å / Num. obs: 41107 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.93	50	98	1	0.063	3.14	7
3.91	4.93	99.6	1	0.055	1.853	6.8
3.42	3.91	99.5	1	0.06	1.586	7.4
3.11	3.42	99.8	1	0.073	1.294	7.5
2.88	3.11	99.8	1	0.084	1.094	7.6
2.71	2.88	99.8	1	0.114	1.014	7.5
2.58	2.71	99.9	1	0.127	0.8	7.6
2.47	2.58	99.9	1	0.142	0.733	7.6
2.37	2.47	99.9	1	0.177	0.723	7.6
2.29	2.37	99.9	1	0.184	0.776	7.7
2.22	2.29	100	1	0.21	0.649	7.7
2.15	2.22	99.9	1	0.254	0.628	7.6
2.1	2.15	100	1	0.333	0.658	7.6
2.05	2.1	100	1	0.373	0.662	7.4
2	2.05	99.6	1	0.452	0.737	6.9

Reflection

Resolution: 2→50 Å / Num. all: 41107 / Num. obs: 41107 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 26.9 Å² / R_merge(I) obs: 0.088 / Χ²: 1.08 / Net I/σ(I): 6.5

Reflection shell

Resolution: 2→2.05 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.452 / Num. unique all: 2712 / Χ²: 0.737 / % possible all: 99.6

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2 Å / D res low: 50 Å / FOM : 0.195 / FOM acentric: 0.213 / FOM centric: 0 / Reflection: 39487 / Reflection acentric: 36218 / Reflection centric: 3269

Phasing MAD set

R cullis acentric: 2.04 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 36218 / Reflection centric: 3269

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
12.5-50	2.81	1	0.3	110	61
7.14-12.5	1.88	0.8	0.4	594	174
5-7.14	2.27	0.6	0.3	1443	261
3.85-5	1.31	0.4	0.3	2719	361
3.12-3.85	1.51	0.3	0.2	4359	453
2.63-3.12	2.35	0.2	0.1	6446	554
2.27-2.63	5.88	0.1	0	8848	646
2-2.27	3.78	0.1	0	11699	759

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z
1	Se	49.28264	0.339	0.664	0.146
2	Se	53.27953	0.061	0.598	0.061
3	Se	43.94408	0.276	0.594	0.155
4	Se	52.55567	0.136	0.452	0.181
5	Se	52.83585	0.195	0.423	0.332
6	Se	61.44001	-0.104	0.711	0.056
7	Se	52.15873	0.134	0.75	0.187
8	Se	59.34769	0.113	0.476	0.369
9	Se	52.59248	-0.116	0.727	0.138
10	Se	43.27251	0.493	0.637	0.234
11	Se	92.14829	-0.325	0.694	0.047
12	Se	75.87262	0.377	0.468	0.388
13	Se	62.03297	0.08	0.376	0.452
14	Se	135.9767	0.045	0.318	0.192
15	Se	74.60677	-0.297	0.809	0.016
16	Se	135.5112	-0.333	0.705	-0.044

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
12.5-50	0.331	0.515	171	110	61
7.14-12.5	0.433	0.56	768	594	174
5-7.14	0.439	0.518	1704	1443	261
3.85-5	0.387	0.438	3080	2719	361
3.12-3.85	0.35	0.387	4812	4359	453
2.63-3.12	0.208	0.226	7000	6446	554
2.27-2.63	0.147	0.157	9494	8848	646
2-2.27	0.068	0.073	12458	11699	759

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 41022

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.8-100	64.4	0.701	502
6.74-8.8	65.9	0.785	610
5.66-6.74	65.2	0.775	745
4.98-5.66	63.8	0.765	817
4.5-4.98	65.2	0.784	933
4.13-4.5	61.9	0.807	1036
3.84-4.13	64.2	0.805	1093
3.61-3.84	61.2	0.804	1168
3.41-3.61	64.5	0.781	1241
3.24-3.41	65.3	0.782	1315
3.1-3.24	64.7	0.739	1374
2.97-3.1	65.3	0.753	1437
2.86-2.97	66.8	0.747	1485
2.76-2.86	70.2	0.743	1532
2.66-2.76	70.2	0.743	1593
2.58-2.66	69.1	0.752	1638
2.51-2.58	70.1	0.745	1706
2.44-2.51	72	0.763	1736
2.37-2.44	70.7	0.757	1807
2.32-2.37	72.2	0.76	1824
2.26-2.32	72.7	0.775	1867
2.21-2.26	73.6	0.753	1925
2.16-2.21	74.1	0.78	1989
2.12-2.16	78	0.744	1982
2.08-2.12	79.7	0.731	2022
2.04-2.08	81.1	0.72	2111
2-2.04	81.6	0.708	2109
1.93-2	89.7	0.631	1425

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2→34.28 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.958 / SU B: 6.082 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.139
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.184	1986	5 %	RANDOM
R_work	0.148	-	-	-
all	0.149	39487	-	-
obs	0.149	39487	99.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 22.009 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7 Å²	0 Å²	0 Å²
2-	-	0.3 Å²	0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: LAST / Resolution: 2→34.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4593	0	35	482	5110

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4743
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3228
X-RAY DIFFRACTION	r_angle_refined_deg	1.386	1.979	6459
X-RAY DIFFRACTION	r_angle_other_deg	0.967	3	7870
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.322	5	631
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.158	22.291	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.591	15	728
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.183	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	725
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5372
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	924
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	955
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	3457
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	2271
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	2334
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	312
X-RAY DIFFRACTION	r_metal_ion_refined	0.184	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.296	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.246	0.2	76
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.194	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.057	1.5	3827
X-RAY DIFFRACTION	r_mcbond_other	0.192	1.5	1266
X-RAY DIFFRACTION	r_mcangle_it	1.201	2	4982
X-RAY DIFFRACTION	r_scbond_it	2.409	3	1760
X-RAY DIFFRACTION	r_scangle_it	3.439	4.5	1473

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.235	143	-
R_work	0.172	2721	-
all	-	2864	-
obs	-	-	99.76 %

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	2.0715	-0.1211	-0.1683	1.5125	0.1411	1.6476	-0.0759	0.0916	-0.1824	-0.1025	-0.0317	0.1849	0.03	-0.2369	0.1075	-0.0655	-0.0235	0.0259	-0.0936	-0.0394	-0.0801	26.0251	58.5084	20.9523
2	1.3037	-0.1741	0.1446	1.0045	0.1901	1.688	-0.0283	0.0841	0.0604	-0.1546	-0.0545	0.075	-0.1265	-0.152	0.0828	-0.0386	0.0212	-0.0226	-0.0776	0.0113	-0.0946	30.6051	93.1547	11.3253
3	1.8502	-0.0421	0.1324	1.4404	0.021	1.5736	0.0528	-0.0474	0.0655	0.0998	-0.0849	0.216	-0.0383	-0.2597	0.0321	-0.0984	0.0094	0.0382	-0.0471	-0.0549	-0.047	15.9711	84.8315	43.2242

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 - 208	23 - 230
2	X-RAY DIFFRACTION	2	B	B	1 - 208	23 - 230
3	X-RAY DIFFRACTION	3	C	C	1 - 208	23 - 230

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