PDB-9zmw: Crystal structure of a Iole protein from Brucella melitensis (ort...

ID or keywords:

Entry

Database: PDB / ID: 9zmw

Title

Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2)

Components

Iole protein

Keywords

BIOSYNTHETIC PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

IolE/MocC family / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / : / Iole protein

Function and homology information

Biological species

Brucella melitensis biotype 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zmw.cif.gz	357.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9zmw.ent.gz	292.7 KB	Display	PDB format
PDBx/mmJSON format	9zmw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zmw_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9zmw_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9zmw_validation.xml.gz	36.8 KB	Display
Data in CIF	9zmw_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/9zmw ftp://data.pdbj.org/pub/pdb/validation_reports/zm/9zmw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: Iole protein

B: Iole protein

C: Iole protein

hetero molecules

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

1

A: Iole protein

hetero molecules

defined by author
Evidence: gel filtration
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Iole protein

hetero molecules

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

3

C: Iole protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.515, 72.154, 239.797
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Iole protein Mass: 34076.559 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M) (bacteria) Strain: ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M / Gene: BMEII0570 / Plasmid: BrmeA.18154.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YCG0
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.08 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: crystal screen C4: 0.2M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20331 C4 drop 1, Puck: PSL-0701, Cryo: direct

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 3, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.3→48.51 Å / Num. obs: 38546 / % possible obs: 100 % / Redundancy: 6.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.159 / R_pim(I) all: 0.069 / R_rim(I) all: 0.173 / Χ²: 0.99 / Net I/σ(I): 9.4 / Num. measured all: 240619
Reflection shell	Resolution: 2.3→2.38 Å / % possible obs: 100 % / Redundancy: 6.2 % / R_merge(I) obs: 1.062 / Num. measured all: 22701 / Num. unique obs: 3690 / CC_1/2: 0.664 / R_pim(I) all: 0.466 / R_rim(I) all: 1.161 / Χ²: 1 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5904: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→47.55 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2352	1824	4.74 %
R_work	0.1852	-	-
obs	0.1877	38448	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→47.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6995	0	3	151	7149

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7154
X-RAY DIFFRACTION	f_angle_d	0.587	9675
X-RAY DIFFRACTION	f_dihedral_angle_d	15.957	2621
X-RAY DIFFRACTION	f_chiral_restr	0.042	1062
X-RAY DIFFRACTION	f_plane_restr	0.005	1285

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.36	0.3141	135	0.2561	2743	X-RAY DIFFRACTION	100
2.36-2.43	0.2728	137	0.2373	2788	X-RAY DIFFRACTION	100
2.43-2.51	0.2991	116	0.2248	2773	X-RAY DIFFRACTION	100
2.51-2.6	0.3213	147	0.2257	2756	X-RAY DIFFRACTION	100
2.6-2.7	0.3121	154	0.222	2808	X-RAY DIFFRACTION	100
2.7-2.83	0.2897	129	0.2226	2776	X-RAY DIFFRACTION	100
2.83-2.98	0.3198	139	0.2158	2777	X-RAY DIFFRACTION	100
2.98-3.16	0.2415	144	0.2108	2809	X-RAY DIFFRACTION	100
3.16-3.41	0.2496	156	0.1932	2798	X-RAY DIFFRACTION	100
3.41-3.75	0.216	135	0.1696	2845	X-RAY DIFFRACTION	100
3.75-4.29	0.2017	146	0.1504	2826	X-RAY DIFFRACTION	100
4.29-5.41	0.1745	150	0.1385	2895	X-RAY DIFFRACTION	100
5.41-47.55	0.1879	136	0.1688	3030	X-RAY DIFFRACTION	99

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	2.2263	0.4388	0.3471	2.9717	0.3897	1.8283	0.1003	-0.0825	-0.2595	0.1425	-0.0406	0.0665	0.1219	0.0457	-0.0765	0.1616	0.0281	0.0132	0.2523	-0.0156	0.28	-16.0199	-26.7946	9.6259
2	1.4402	-0.2732	-1.3719	1.8927	0.4897	3.7034	0.1486	-0.087	-0.2325	0.0321	-0.0225	-0.0215	-0.09	0.1365	-0.091	0.1477	0.0275	-0.0194	0.2379	-0.0125	0.3015	-13.2513	-28.9261	20.3571
3	2.5424	-0.7791	-0.9624	2.4801	0.2716	1.9196	-0.0928	0.0416	-0.0282	0.3804	0.0907	-0.0132	-0.0448	-0.04	0.0087	0.1989	0.0072	-0.0475	0.282	0.0539	0.2629	-12.7536	-27.6162	29.0062
4	2.7568	-0.7621	1.3265	2.6276	0.5661	6.0285	-0.2483	-0.3897	-0.1651	-0.0074	0.1045	0.3238	-0.0235	-0.524	0.1529	0.2255	-0.0157	0.0766	0.415	-0.0086	0.3311	-34.0259	-17.3678	25.278
5	2.0477	0.6342	-0.1119	1.569	0.1563	2.0779	0.0548	-0.3423	0.1149	0.144	0.0101	0.1383	-0.2906	-0.3179	-0.06	0.2079	0.047	0.0013	0.2903	-0.0157	0.242	-18.4847	-16.6995	31.8794
6	2.4119	-0.8036	1.4066	2.2274	-0.5526	5.1299	0.0505	-0.0437	0.1707	0.2802	0.0194	-0.2532	-0.1195	0.32	-0.0455	0.2286	0.0054	-0.0018	0.2181	-0.033	0.2967	-19.1877	-8.7824	26.5157
7	3.0976	0.395	0.3443	4.6866	0.7041	5.6288	0.2024	-0.0285	0.2572	0.1869	-0.1089	-0.3347	-0.4611	-0.0146	-0.0785	0.1866	-0.0389	0.0183	0.2116	0.0129	0.2262	-13.0515	-6.5167	21.9605
8	4.857	-0.8289	-1.2756	1.926	-0.3735	2.7519	-0.088	0.0214	0.2795	0.2249	0.1544	0.3529	-0.2903	-0.1181	-0.0403	0.2252	0.0146	-0.0506	0.2938	-0.0419	0.3642	-32.9891	-11.7151	11.2403
9	4.2913	-0.5564	0.9544	2.8001	-0.612	3.788	-0.3013	0.4726	0.8861	-0.3781	0.1016	0.1255	-0.4487	0.229	0.1882	0.2366	-0.0179	-0.0072	0.2105	0.0064	0.2892	-16.2931	-6.305	9.8298
10	3.2493	-0.2892	1.1677	0.8315	-0.4146	2.5993	-0.041	-0.0556	-0.0693	-0.1547	0.0391	0.1129	-0.1797	0.0168	0.0119	0.1928	0.0284	-0.0369	0.2467	-0.0367	0.3231	-16.29	-16.7448	10.3169
11	1.5787	0.3388	-0.1073	4.3	0.8465	3.2125	0.2095	0.1629	0.1529	-0.1182	0.029	-0.2195	-0.266	0.2895	-0.2396	0.1729	-0.0431	0.0371	0.2927	0.0369	0.2539	-9.9716	-11.7779	4.0952
12	1.3911	-0.0575	-0.247	3.8292	-0.9316	2.7587	0.0565	-0.2429	0.0841	-0.0352	0.0513	-0.1244	0.0065	0.1154	-0.1155	0.2048	-0.0013	-0.0221	0.3467	0.0362	0.2727	-6.8767	21.4013	50.4835
13	2.7959	0.5739	-0.4001	2.8229	-0.1851	2.2213	0.1086	0.0812	0.2814	0.0447	0.1325	0.2657	-0.1924	-0.0107	-0.2416	0.1922	0.0141	-0.0295	0.3161	0.0527	0.3278	-11.6211	26.2659	50.027
14	2.4584	-0.6257	1.3952	2.9607	-1.7841	4.3225	0.343	0.3089	0.1922	-0.111	-0.1964	0.1191	0.0914	0.0346	-0.1857	0.1864	0.0337	-0.0065	0.2197	0.0245	0.2363	-12.0492	24.7744	61.3073
15	4.0105	-2.0984	0.3273	4.1548	-0.6105	2.9768	-0.0464	-0.0114	0.0217	0.5998	0.0526	0.0159	-0.2314	-0.0799	-0.0016	0.312	-0.0159	0.0271	0.2683	0.013	0.2703	-12.6482	22.4087	69.7873
16	1.7701	0.1892	-0.8353	3.4944	-1.5272	4.178	-0.0653	-0.297	-0.3398	0.0289	-0.191	-0.6754	-0.015	0.3262	0.2294	0.2839	-0.0031	-0.1304	0.4456	0.0736	0.4228	8.7513	13.0915	64.8496
17	0.739	-0.3744	-0.0391	1.9063	-0.3365	2.8406	0.019	-0.0822	-0.1858	0.2442	0.0179	-0.0948	0.3471	-0.0828	-0.0356	0.2631	-0.0207	-0.078	0.2286	0.047	0.2385	-7.5891	6.7162	66.8341
18	7.0384	-1.561	0.9969	2.1288	-0.2798	2.9541	0.0132	-0.0848	-0.2658	0.0623	-0.0744	-0.2614	0.2549	0.3511	0.0256	0.2323	0.0142	-0.0096	0.343	0.0767	0.3602	7.2453	8.7388	50.0907
19	2.0869	-0.6625	-0.5813	1.1662	-0.3921	2.9985	0.0097	0.1925	-0.2263	-0.2628	0.0555	0.0387	0.2323	-0.1865	-0.0748	0.2335	-0.059	-0.046	0.2537	0.0221	0.3144	-8.8526	8.3897	48.9749
20	2.9875	0.8434	-0.2845	2.5627	0.1657	0.1166	0.1066	0.2743	0.0407	-0.2318	0.1799	0.3335	0.3899	-0.5387	-0.1684	0.2776	-0.1357	-0.1385	0.4016	0.0699	0.3257	-15.5175	9.4108	43.3343
21	2.7428	-0.3507	0.0372	3.2316	-0.4708	2.1272	0.2197	0.0659	-0.2149	-0.4387	-0.08	-0.0385	0.2731	0.1185	-0.1262	0.3072	-0.0131	-0.0736	0.2937	0.0371	0.2781	-33.2895	8.8337	29.0715
22	1.4826	0.6485	0.1196	1.331	-0.0369	1.4196	-0.1828	0.1395	-0.347	-1.2233	0.0707	-0.1009	0.3741	-0.1045	-0.1145	0.8224	-0.0358	-0.0143	0.2146	-0.0247	0.2608	-30.6743	15.2853	12.1848
23	2.3678	-0.9331	1.5595	0.5378	-0.0328	3.7707	0.0066	0.1848	0.2878	-1.0207	-0.0996	0.0142	-0.3246	0.2854	0.0801	0.6201	-0.057	-0.0379	0.2374	0.0294	0.2991	-30.3591	28.9145	14.5311
24	2.3988	-0.0315	0.4481	2.3618	-1.1483	2.3539	0.0971	-0.1968	0.0018	-0.1786	-0.0096	-0.0159	-0.0371	-0.055	-0.0888	0.2425	0.0019	-0.0114	0.213	-0.0274	0.1946	-31.0369	24.9569	29.6466

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 77 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 104 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 105 through 124 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 125 through 161 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 162 through 191 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 208 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 209 through 232 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 233 through 256 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 257 through 275 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 276 through 299 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 24 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 25 through 49 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 50 through 77 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 78 through 104 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 105 through 124 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 125 through 207 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 208 through 232 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 233 through 275 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 276 through 299 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 0 through 49 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 50 through 161 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 162 through 191 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 192 through 298 )

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