PDB-3iac: 2.2 Angstrom Crystal Structure of Glucuronate Isomerase from Salm...

ID or keywords:

Entry

Database: PDB / ID: 3iac

Title

2.2 Angstrom Crystal Structure of Glucuronate Isomerase from Salmonella typhimurium.

Components

Glucuronate isomerase

Keywords

ISOMERASE /

Glucuronate Isomerase / idp02065 /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

glucuronate isomerase /

glucuronate isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process
Similarity search - Function

Biological species

Salmonella Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.22 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.2 Angstrom Crystal Structure of Glucuronate Isomerase from Salmonella typhimurium.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jul 13, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3iac.cif.gz	311.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3iac.ent.gz	264.4 KB	Display	PDB format
PDBx/mmJSON format	3iac.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	4i6v-d 1j5s-d 4qsm-1 2brx-1 5j6f-1 2ji5-1 4m3u-d 6qpx-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
Other databases	TargetDB: idp02065

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Glucuronate isomerase

B: Glucuronate isomerase

C: Glucuronate isomerase

hetero molecules

164 kDa, 3 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)	225.535, 225.535, 82.745
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Glucuronate isomerase / / Uronate isomerase / Uronic isomerase Mass: 54691.254 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella Typhimurium (bacteria) / Strain: LT2 / Gene: STM3137, uxaC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q8ZM23, glucuronate isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1134 / 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: 3.21 Å³/Da / Density % sol: 61.64 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 0.2M Ammonium Acetate, 0.1M Bis-Tris (pH 6.5), 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2009 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.22→50 Å / Num. all: 104505 / Num. obs: 104505 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / B_iso Wilson estimate: 27.4 Å² / R_merge(I) obs: 0.144 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.22→2.26 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5151 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
CRANK		phasing
REFMAC	5.5.0088	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.22→29.76 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.946 / SU B: 8.691 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Isotropic Temperature Factors Refined
Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18094	5227	5 %	RANDOM
R_work	0.14378	-	-	-
all	0.14565	99164	-	-
obs	0.14565	99164	99.79 %	-

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: 15.161 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	-0 Å²	-0 Å²
2-	-	0.91 Å²	0 Å²
3-	-	-	-1.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→29.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11290	0	3	1134	12427

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	11792
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8059
X-RAY DIFFRACTION	r_angle_refined_deg	1.399	1.943	16015
X-RAY DIFFRACTION	r_angle_other_deg	0.886	3	19450
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.462	5	1444
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.816	23.52	608
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.355	15	1984
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.427	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1706
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	13381
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2576
X-RAY DIFFRACTION	r_mcbond_it	0.877	1.5	7120
X-RAY DIFFRACTION	r_mcbond_other	0.251	1.5	2898
X-RAY DIFFRACTION	r_mcangle_it	1.595	2	11467
X-RAY DIFFRACTION	r_scbond_it	2.993	3	4672
X-RAY DIFFRACTION	r_scangle_it	4.586	4.5	4548

LS refinement shell

Resolution: 2.22→2.282 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	386	-
R_work	0.213	7045	-
obs	-	7045	97.67 %

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	0.8908	-0.3559	-0.3561	0.8563	0.2892	0.4722	0.0257	0.1022	-0.0119	-0.0975	-0.0389	-0.0149	-0.0421	0.0121	0.0132	0.047	0.0178	0.0298	0.0303	0.0116	0.0462	93.8893	17.2501	-3.6426
2	1.6203	0.118	-0.5035	0.9252	-0.0228	0.7101	0.0048	0.1489	-0.1156	-0.0818	-0.0332	-0.0285	-0.0277	-0.0369	0.0285	0.0673	0.0516	0.0213	0.0633	-0.0077	0.0366	90.8414	5.3869	-8.7502
3	1.7088	-0.2579	0.1046	0.9373	-0.5121	1.9869	-0.0202	-0.0107	-0.0799	0.0253	-0.0268	-0.1316	0.0288	0.0643	0.047	0.0054	0.0046	-0.0136	0.0069	-0.0075	0.0575	99.0214	8.7606	23.1609
4	0.8528	-0.184	0.2092	0.6672	-0.0235	0.8804	-0.0394	-0.1245	-0.0452	0.0618	0.0012	-0.0266	-0.0467	-0.0387	0.0382	0.0424	0.0364	0.0072	0.0548	0.0066	0.0368	82.583	14.897	21.4636
5	1.8219	-0.7021	-0.2609	0.7523	-0.1465	0.861	0.0584	0.0591	0.2211	-0.0385	-0.0884	-0.1021	-0.1672	-0.0163	0.0301	0.0611	0.0248	0.0126	0.0196	0.0165	0.0483	88.1678	29.4141	3.1017
6	0.8808	-0.002	0.1047	0.8663	-0.0324	0.6874	0.038	0.0173	0.1863	0.0654	-0.0287	-0.1245	-0.2256	-0.0274	-0.0093	0.1866	0.1076	0.0123	0.0979	0.0025	0.1543	65.0521	49.627	9.6807
7	1.0743	-0.4492	0.0919	1.0801	0.0459	1.3417	0.02	-0.0203	0.3435	0.075	0.0235	-0.2508	-0.174	0.0899	-0.0434	0.193	0.0473	-0.0016	0.029	-0.0209	0.1894	77.1394	51.2869	14.8109
8	0.9961	-0.5292	-0.1908	3.2879	-1.5133	2.3208	-0.048	-0.1855	0.1063	0.2077	0.0254	-0.0153	-0.2504	0.0393	0.0226	0.1357	0.113	-0.0042	0.1592	-0.05	0.0806	55.2872	43.4235	31.1127
9	0.7865	-0.2582	-0.2041	0.4614	0.1796	0.4976	-0.0358	-0.1082	-0.0298	0.1238	0.0487	0.0535	-0.0544	-0.0708	-0.0129	0.126	0.1044	0.0143	0.117	-0.0018	0.0486	54.9853	28.9253	26.821
10	1.0025	-0.0273	0.1212	1.1398	0.1883	0.506	0.0718	0.0789	0.0311	-0.0523	-0.0836	0.0212	-0.1106	-0.1059	0.0118	0.1254	0.123	0.0161	0.1242	0.0029	0.068	55.9395	39.2109	3.5799
11	1.9131	-0.4156	0.0011	0.7898	0.2968	0.7967	0.1372	0.2205	-0.2254	-0.1211	-0.1751	0.2075	-0.1176	-0.2434	0.0379	0.0967	0.1275	-0.059	0.2002	-0.1007	0.1118	49.9613	13.0387	-13.4988
12	1.4266	-0.4769	-0.4223	0.9259	0.4006	1.4506	0.1441	0.2581	-0.1626	-0.0751	-0.115	0.194	-0.0689	-0.287	-0.0292	0.0724	0.1105	-0.0576	0.1973	-0.0611	0.1063	39.8328	20.9022	-8.4404
13	1.9418	-0.4128	0.8516	1.5327	0.0658	2.4708	0.052	-0.1756	-0.4481	0.1048	-0.0145	0.4134	0.1958	-0.4011	-0.0375	0.0389	-0.0396	0.0721	0.1095	-0.0197	0.3541	49.1163	-7.8525	9.2718
14	0.9533	-0.4991	-0.1118	0.626	-0.0496	0.453	0.0035	0.0462	-0.2381	-0.0067	-0.0527	0.1963	0.0641	-0.1063	0.0491	0.0483	0.0164	0.0045	0.0628	-0.0343	0.1024	60.4825	4.6507	6.8605
15	2.2263	0.5816	-0.2396	1.5505	-0.433	1.1483	0.0565	0.2429	-0.0956	-0.1399	-0.1355	0.0117	-0.0078	-0.1004	0.079	0.0893	0.0918	-0.0397	0.1303	-0.0682	0.0531	62.9216	9.6097	-12.7176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 59
2	X-RAY DIFFRACTION	2	A	60 - 152
3	X-RAY DIFFRACTION	3	A	153 - 235
4	X-RAY DIFFRACTION	4	A	236 - 395
5	X-RAY DIFFRACTION	5	A	396 - 470
6	X-RAY DIFFRACTION	6	B	2 - 58
7	X-RAY DIFFRACTION	7	B	59 - 152
8	X-RAY DIFFRACTION	8	B	153 - 204
9	X-RAY DIFFRACTION	9	B	205 - 394
10	X-RAY DIFFRACTION	10	B	395 - 470
11	X-RAY DIFFRACTION	11	C	3 - 58
12	X-RAY DIFFRACTION	12	C	59 - 152
13	X-RAY DIFFRACTION	13	C	153 - 272
14	X-RAY DIFFRACTION	14	C	273 - 404
15	X-RAY DIFFRACTION	15	C	405 - 470

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