PDB-4zm5: Shigella flexneri lipopolysaccharide O-antigen chain-length regul...

ID or keywords:

Entry

Database: PDB / ID: 4zm5

Title

Shigella flexneri lipopolysaccharide O-antigen chain-length regulator WzzBSF - A107P mutant

Components

Chain length determinant protein

Keywords

MEMBRANE PROTEIN / lipopolysaccharide / chain-length / virulence / serospecificity

Function / homology

Function and homology information

lipopolysaccharide biosynthetic process / plasma membrane
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Ericsson, D.J. / Chang, C.-W. / Lonhienne, T. / Casey, L. / Benning, F. / Kobe, B. / Tran, E.N.H. / Morona, R.

Citation

Journal: Plos One / Year: 2015
Title: Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri.
Authors: Chang, C.W. / Tran, E.N. / Ericsson, D.J. / Casey, L.W. / Lonhienne, T. / Benning, F. / Morona, R. / Kobe, B.

History

Deposition	May 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zm5.cif.gz	291.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4zm5.ent.gz	238.8 KB	Display	PDB format
PDBx/mmJSON format	4zm5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4zm5_validation.pdf.gz	445.8 KB	Display	wwPDB validaton report
Full document	4zm5_full_validation.pdf.gz	450.2 KB	Display
Data in XML	4zm5_validation.xml.gz	25.9 KB	Display
Data in CIF	4zm5_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/4zm5 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zm5	HTTPS FTP

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Related structure data

Related structure data	4zm1C 3b8pS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zm1-d 4e2h-d 4bfb-d 3ry3-d 3do9-d 2oxh-d 5m6a-d 0927 4fmt-d 6o1f-d 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

Deposited unit

A: Chain length determinant protein

B: Chain length determinant protein

C: Chain length determinant protein

hetero molecules

82.8 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)	80.570, 62.460, 90.240
Angle α, β, γ (deg.)	90.00, 94.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chain length determinant protein / Polysaccharide antigen chain regulator Mass: 27592.945 Da / Num. of mol.: 3 / Fragment: UNP residues 54-293 / Mutation: A107P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: RMA4053 / Gene: wzzB, cld, rol, SF2089, S2210 / Variant: serotype Y wzz::kanr / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37792
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.72 Å³/Da / Density % sol: 54.8 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 18% peg400, 18% peg8k, 0.1M MgCl2, 0.1 M citric-acid/HEPES/CHES buffer (pH 7.3)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2011
Radiation	Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.01→90.01 Å / Num. obs: 57620 / % possible obs: 96.7 % / Redundancy: 3.1 % / B_iso Wilson estimate: 48.63 Å² / R_merge(I) obs: 0.223 / Net I/σ(I): 4.1
Reflection shell	Resolution: 2.01→2.06 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 0.2 / % possible all: 82

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Processing

Software

Name	Version	Classification
Coot	0.7	model building
BUSTER	2.10.0	refinement
PHASER	2.3.0	phasing
XSCALE	July 4, 2012	data scaling
XDS	July 4, 2012	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3B8P

3b8p

Resolution: 2.47→32.14 Å / Cor.coef. F_o:F_c: 0.9307 / Cor.coef. F_o:F_c free: 0.9055 / SU R Cruickshank DPI: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.374 / SU R_free Blow DPI: 0.249 / SU R_free Cruickshank DPI: 0.255

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	1592	5.03 %	RANDOM
R_work	0.1951	-	-	-
obs	0.1975	31641	97.66 %	-

Displacement parameters

B_iso mean: 52.03 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.8315 Å²	0 Å²	-1.0701 Å²
2-	-	-0.2274 Å²	0 Å²
3-	-	-	7.0589 Å²

Refine analyze

Luzzati coordinate error obs: 0.363 Å

Refinement step

Cycle: 1 / Resolution: 2.47→32.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5556	0	2	141	5699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	5637	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.08	7639	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2729	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		209	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		772	HARMONIC	5
X-RAY DIFFRACTION	t_it		5637	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	2.67
X-RAY DIFFRACTION	t_other_torsion	3.25
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		758	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		6446	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.47→2.55 Å / Total num. of bins used: 16

	R_factor	Num. reflection	% reflection
R_free	0.2987	146	5 %
R_work	0.2294	2775	-
all	0.2326	2921	-
obs	-	-	97.66 %

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	0.4446	0.7305	-1.3719	1.6048	-0.2471	4.8554	-0.08	-0.1905	-0.0235	-0.1992	-0.0407	-0.1073	-0.0364	0.5833	0.1207	-0.2401	0.0104	0.0319	-0.0284	0.055	-0.1726	69.9673	6.958	70.4539
2	0.9826	-0.8854	1.9466	0	-3.0025	5.5891	0.059	-0.0699	-0.0192	-0.1676	-0.1525	0.0149	0.2344	0.1692	0.0935	0.1437	0.0211	-0.0121	-0.0779	0.0571	-0.0795	67.3029	17.3969	38.9563
3	1.2966	-0.4434	2.1233	2.2983	-0.6656	6.3691	-0.1238	0.2447	0.2865	-0.5464	0.0016	0.0747	0.0089	0.106	0.1222	-0.1518	-0.03	0.0504	-0.1627	0.05	-0.1646	52.2152	34.9158	3.2253
4	2.2222	-0.5029	3.9482	0.5552	-1.446	7.6412	-0.0514	-0.0824	0.0103	0.332	-0.0759	-0.0361	-0.2713	0.0421	0.1272	0.1908	-0.012	0.0149	-0.0209	0.0181	-0.0116	60.0297	31.4416	26.1539
5	0.1469	0.6928	-1.1253	0	3.5041	2.5549	-0.126	-0.5283	-0.1152	-0.1525	0.2058	-0.0715	-0.0499	0.5384	-0.0797	-0.2324	0.0007	0.0268	0.1242	0.1154	-0.1918	71.5198	10.089	81.5869
6	1.4566	0.6924	-0.8118	1.6203	-0.9075	3.8111	-0.0884	0.1455	0.1184	-0.1671	0.1395	0.1208	-0.1015	0.094	-0.0511	-0.196	0.0164	0.0209	-0.2427	-0.0175	-0.1974	52.2283	13.2107	81.7631
7	0.177	0.3077	1.0146	0.0064	-2.6293	4.1033	0.0425	-0.0146	0.0601	-0.2323	-0.0738	0.1053	-0.1484	0.5407	0.0313	0.3044	0.0217	0.0486	-0.2086	-0.0006	-0.1226	58.4278	30.1334	59.2036
8	4.0387	-1.4886	2.5717	6.715	0.0186	4.0465	0.0131	0.0466	0.3597	0.1855	-0.2723	0.1574	-0.9041	0.0785	0.2592	0.2198	-0.0519	-0.0257	-0.0654	0.027	0.0046	56.6871	45.8697	19.0655
9	1.9944	1.4049	-6.8275	3.5833	-0.2589	2.1517	-0.0879	0.3694	0.1283	-0.3741	0.1268	0.2264	-0.3665	-0.3616	-0.0389	0.3602	0.0416	0.0264	0.0804	0.2621	-0.0018	51.3741	37.8526	55.3649
10	2.3556	2.2558	-2.9923	0	1.4709	1.2222	0.0114	-0.1724	-0.1411	0.1231	-0.0096	0.133	0.1649	-0.1936	-0.0018	-0.1102	0.0147	0.0231	-0.1698	0.0172	-0.2027	45.6663	11.1277	90.8957
11	0.9757	0.2875	1.5033	0.6876	-1.9041	8.6464	-0.0998	0.0287	-0.1141	-0.319	-0.002	0.0148	1.1635	0.2379	0.1017	0.2226	0.1429	0.1044	-0.1121	0.011	-0.1577	65.5823	-6.1107	55.2352
12	1.0934	-2.8105	2.4846	3.516	-4.8122	5.6786	0.0064	-0.1847	-0.0795	-0.0461	0.1713	0.2145	0.5449	-0.2634	-0.1778	0.2961	-0.0343	0.0028	-0.0942	0.0376	-0.0967	53.3329	2.8216	28.3737
13	6.4758	-0.4459	1.5204	1.6843	0.2118	2.6108	-0.2068	0.2307	0.1039	-0.4072	0.0047	0.2628	-0.1085	0.0182	0.2021	-0.132	0.0173	-0.0018	-0.1838	0.0012	-0.1294	38.4629	32.215	0.9812
14	2.1236	-1.4715	2.3749	2.2019	-3.626	10.4489	-0.0771	-0.2873	0.0014	0.4322	-0.1264	-0.0172	0.2079	0.1294	0.2035	0.0757	-0.0236	0.0541	-0.0854	0.0294	-0.0882	56.0073	13.5923	20.9738
15	5.0432	0.4621	3.7327	0	1.6662	0.9036	-0.058	-0.028	-0.1789	-0.115	0.139	-0.0284	0.3114	0.507	-0.081	0.1253	0.3542	0.1555	0.0804	0.1502	-0.1504	74.1123	-8.3944	58.9081

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ B\|5 - 105 }
2	X-RAY DIFFRACTION	2	{ B\|106 - 147 }
3	X-RAY DIFFRACTION	3	{ B\|148 - 167 }
4	X-RAY DIFFRACTION	4	{ B\|168 - 224 }
5	X-RAY DIFFRACTION	5	{ B\|225 - 241 }
6	X-RAY DIFFRACTION	6	{ A\|5 - 102 }
7	X-RAY DIFFRACTION	7	{ A\|103 - 145 }
8	X-RAY DIFFRACTION	8	{ A\|146 - 193 }
9	X-RAY DIFFRACTION	9	{ A\|194 - 224 }
10	X-RAY DIFFRACTION	10	{ A\|225 - 240 }
11	X-RAY DIFFRACTION	11	{ C\|5 - 102 }
12	X-RAY DIFFRACTION	12	{ C\|103 - 146 }
13	X-RAY DIFFRACTION	13	{ C\|147 - 191 }
14	X-RAY DIFFRACTION	14	{ C\|192 - 221 }
15	X-RAY DIFFRACTION	15	{ C\|222 - 240 }

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