PDB-3k3s: Crystal structure of altronate hydrolase (fragment 1-84) from Shi...

ID or keywords:

Entry

Database: PDB / ID: 3k3s

Title

Crystal structure of altronate hydrolase (fragment 1-84) from Shigella Flexneri.

Components

Altronate hydrolase

Keywords

HYDROLASE / altronate hydrolase / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity / lyase activity
Similarity search - Function

Biological species

Shigella flexneri 2a str. 2457T (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.15 Å

Authors

Hou, J. / Chruszcz, M. / Xu, X. / Le, B. / Zimmerman, M.D. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of altronate hydrolase (fragment 1-84) from Shigella Flexneri.
Authors: Hou, J. / Chruszcz, M. / Xu, X. / Le, B. / Zimmerman, M.D. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W.

History

Deposition	Oct 4, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Apr 29, 2015	Group: Non-polymer description
Revision 1.3	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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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PDBx/mmCIF format	3k3s.cif.gz	152.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3k3s_validation.pdf.gz	520.2 KB	Display	wwPDB validaton report
Full document	3k3s_full_validation.pdf.gz	526.4 KB	Display
Data in XML	3k3s_validation.xml.gz	32.9 KB	Display
Data in CIF	3k3s_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/3k3s ftp://data.pdbj.org/pub/pdb/validation_reports/k3/3k3s	HTTPS FTP

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Related structure data

Similar structure data	3can-d 1cvj-1 3ofe-d 4f0d-2 2r2i-d 3c7m-2 4k6x-1 3dnj-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) 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: APC28040.2

Similar structure data

Other databases

TargetDB: APC28040.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Altronate hydrolase

B: Altronate hydrolase

C: Altronate hydrolase

D: Altronate hydrolase

E: Altronate hydrolase

F: Altronate hydrolase

G: Altronate hydrolase

H: Altronate hydrolase

hetero molecules

92.9 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Altronate hydrolase

D: Altronate hydrolase

hetero molecules

defined by author&software
23.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Altronate hydrolase

E: Altronate hydrolase

hetero molecules

defined by author&software
23.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Altronate hydrolase

H: Altronate hydrolase

hetero molecules

defined by author&software
23.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: Altronate hydrolase

G: Altronate hydrolase

hetero molecules

defined by author&software
23.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	113.968, 40.218, 121.001
Angle α, β, γ (deg.)	90.00, 104.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 84
2	1	1	4	B	1 - 84
3	1	1	4	C	1 - 84
4	1	1	4	D	1 - 84
5	1	1	4	E	1 - 84
6	1	1	4	F	1 - 84
7	1	1	4	G	1 - 84
8	1	1	4	H	1 - 84

#1: Protein	Altronate hydrolase Mass: 11528.559 Da / Num. of mol.: 8 / Fragment: residues 1-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria) Gene: S3338, SF3131, uxaA / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q83JJ2, UniProt: A0A0H2VY20*PLUS
#2: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.91 Å³/Da / Density % sol: 57.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1 M HEPES pH=7.0, 5% tacsimate pH=7.0, 10% PEG 5K MME, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008 / Details: MIRROR
Radiation	Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. all: 59149 / Num. obs: 59149 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 32.7 Å² / R_merge(I) obs: 0.095 / R_sym value: 0.095 / Net I/σ(I): 18.184
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.535 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2907 / R_sym value: 0.535 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-3000		phasing
MLPHARE		phasing
DM		model building
SHELXD		phasing
RESOLVE		model building
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.15→50 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.94 / SU B: 8.799 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.213	2965	5 %	RANDOM
R_work	0.174	-	-	-
all	0.176	58766	-	-
obs	0.176	58766	99.8 %	-

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: 15.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7 Å²	0 Å²	0.96 Å²
2-	-	1.44 Å²	0 Å²
3-	-	-	-1.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5077	0	41	613	5731

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	5202
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	3197
X-RAY DIFFRACTION	r_angle_refined_deg	1.514	1.939	7068
X-RAY DIFFRACTION	r_angle_other_deg	0.87	3	7866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.986	5	675
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.157	24.672	229
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.712	15	821
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.88	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	849
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5934
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	983
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.695	1.5	3375
X-RAY DIFFRACTION	r_mcbond_other	0.203	1.5	1401
X-RAY DIFFRACTION	r_mcangle_it	1.252	2	5354
X-RAY DIFFRACTION	r_scbond_it	2.17	3	1827
X-RAY DIFFRACTION	r_scangle_it	3.37	4.5	1714
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 / Ens-ID: 1 / Number: 959 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.64	0.5
B	medium positional	0.61	0.5
C	medium positional	0.75	0.5
D	medium positional	0.65	0.5
E	medium positional	0.58	0.5
F	medium positional	0.96	0.5
G	medium positional	0.81	0.5
H	medium positional	1.1	0.5
A	medium thermal	0.99	2
B	medium thermal	0.97	2
C	medium thermal	0.76	2
D	medium thermal	0.82	2
E	medium thermal	0.75	2
F	medium thermal	0.73	2
G	medium thermal	0.8	2
H	medium thermal	0.81	2

LS refinement shell

Resolution: 2.15→2.21 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.274	210	-
R_work	0.225	4081	-
obs	-	-	99.79 %

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	2.3719	-0.4621	-0.1164	1.9806	0.5439	2.4812	-0.2038	-0.3846	-0.142	0.1163	0.1652	0.1574	0.242	0.3041	0.0386	0.0626	0.0591	0.0389	0.1689	0.0299	0.0382	-26.983	-2.251	62.286
2	3.1459	0.0304	-1.6135	0.9664	0.7023	2.3975	-0.0196	-0.086	0.1471	-0.1172	0.069	0.0367	-0.1337	0.1551	-0.0494	0.0489	-0.0059	0.0147	0.0609	-0.0025	0.0211	-23.989	3.009	51.26
3	2.5878	0.686	-0.754	0.9479	1.2953	8.5505	-0.2339	-0.0617	-0.5178	0.0412	-0.0943	-0.1342	1.3706	-0.0992	0.3282	0.3615	-0.0069	0.1182	0.0513	0.0156	0.1226	-7.662	-15.085	32.262
4	2.0951	-0.5007	-1.2051	1.3039	0.1251	3.2017	-0.1455	0.1123	-0.0257	-0.1381	-0.0181	0.0309	0.253	-0.1907	0.1636	0.1163	-0.0505	0.041	0.0668	-0.0152	0.0285	-15.407	-5.781	32.762
5	3.8912	0.2016	0.4482	1.1425	-0.0819	2.7895	-0.0186	0.6852	0.1234	-0.2343	-0.0474	-0.1332	0.018	0.1612	0.066	0.0628	0.0139	0.0262	0.17	0.0627	0.1866	30.645	-4.677	46.413
6	4.6813	2.4809	-0.8064	1.9012	-0.8452	3.3545	0.0258	0.2075	0.5872	0.0195	0.123	0.1636	-0.2574	-0.221	-0.1488	0.0384	0.0219	0.0281	0.0467	0.0454	0.2358	21.908	-3.373	55.346
7	7.0298	-2.1439	-2.749	2.2126	2.7028	6.557	-0.2442	0.7496	-1.4331	0.0481	-0.3436	0.6915	0.6499	-0.6738	0.5878	0.1326	-0.0803	0.0347	0.133	-0.1677	0.4464	-43.721	-9.552	45.979
8	4.1084	-1.9375	-0.548	2.2825	0.2982	0.6172	0.1128	0.5278	-0.0477	-0.2394	-0.1854	0.1041	-0.0744	-0.1052	0.0726	0.0407	-0.0048	-0.0045	0.1248	-0.0315	0.1046	-44.433	2.862	46.288
9	4.0702	-0.8878	-2.9594	4.8253	3.2748	5.1195	0.0504	-0.62	0.1184	0.2383	0.1909	-0.4479	0.1945	0.8084	-0.2412	0.1105	-0.0075	0.0209	0.2471	-0.0169	0.0619	5.143	3.299	41.083
10	1.4116	-0.171	-1.943	1.1638	0.4713	5.4359	0.1546	0.0879	0.2334	-0.2305	0.0138	0.0387	-0.4418	0.0382	-0.1684	0.1793	-0.0151	0.0723	0.1128	0.0042	0.0943	0.861	7.307	30.403
11	4.1584	-0.8803	-0.0728	2.3659	-0.4631	3.5538	0.127	0.6418	0.0148	-0.1988	-0.1117	0.3761	-0.09	-0.5544	-0.0153	0.1873	0.0323	0.0354	0.2748	-0.006	0.104	-16.749	-1.739	0.811
12	3.7956	-0.6274	-0.9699	1.6069	-1.2375	6.6335	0.1892	0.0497	0.3666	0.192	-0.1348	0.158	-0.4397	-0.4138	-0.0544	0.2151	-0.0071	0.0731	0.1701	-0.0209	0.0924	-15.998	0.178	12.812
13	1.9146	0.3919	2.1066	2.2625	-0.5956	4.4264	0.0654	0.313	-0.15	-0.1912	0.003	-0.2454	0.1857	0.6359	-0.0683	0.1666	0.0149	0.0797	0.184	-0.02	0.0618	7.738	0.471	6.935
14	0.5642	0.4477	0.2717	3.0585	-0.388	2.7131	0.0115	-0.0462	0.1113	0.1508	-0.0565	0.1802	-0.1894	-0.0933	0.0449	0.1774	0.0009	0.0689	0.1305	0.0101	0.0534	1.738	10.744	9.712
15	1.1254	0.7385	-0.0028	2.2955	-0.4098	3.1747	0.1033	-0.306	-0.1266	0.2418	-0.1373	-0.3578	0.1383	0.298	0.034	0.0636	-0.009	-0.02	0.1461	0.0257	0.2238	41.247	-2.562	69.302
16	1.9446	1.782	0.2311	3.3276	-0.1999	1.4216	0.0542	-0.0629	0.3005	0.1288	0.0113	0.408	-0.1709	-0.225	-0.0655	0.0391	0.0212	0.0304	0.0809	-0.0018	0.2306	35.669	7.973	66.536

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 35
2	X-RAY DIFFRACTION	2	A	36 - 84
3	X-RAY DIFFRACTION	3	B	0 - 35
4	X-RAY DIFFRACTION	4	B	36 - 84
5	X-RAY DIFFRACTION	5	C	0 - 35
6	X-RAY DIFFRACTION	6	C	36 - 84
7	X-RAY DIFFRACTION	7	D	0 - 35
8	X-RAY DIFFRACTION	8	D	36 - 84
9	X-RAY DIFFRACTION	9	E	0 - 35
10	X-RAY DIFFRACTION	10	E	36 - 84
11	X-RAY DIFFRACTION	11	F	0 - 35
12	X-RAY DIFFRACTION	12	F	36 - 84
13	X-RAY DIFFRACTION	13	G	0 - 35
14	X-RAY DIFFRACTION	14	G	36 - 84
15	X-RAY DIFFRACTION	15	H	0 - 35
16	X-RAY DIFFRACTION	16	H	36 - 84

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