PDB-4zm1: Shigella flexneri lipopolysaccharide O-antigen chain-length regul...

ID or keywords:

Entry

Database: PDB / ID: 4zm1

Title

Shigella flexneri lipopolysaccharide O-antigen chain-length regulator WzzBSF - wild type

Components

Chain length determinant protein

Keywords

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

Function / homology

Function and homology information

lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / plasma membrane
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

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

Funding support

Australia, 1items

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, 2017	Group: Author supporting evidence / Data collection / Derived calculations Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zm1.cif.gz	297.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4zm1.ent.gz	244.8 KB	Display	PDB format
PDBx/mmJSON format	4zm1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4zm1_validation.pdf.gz	459.4 KB	Display	wwPDB validaton report
Full document	4zm1_full_validation.pdf.gz	467.4 KB	Display
Data in XML	4zm1_validation.xml.gz	26 KB	Display
Data in CIF	4zm1_validation.cif.gz	35.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/4zm1 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zm1	HTTPS FTP

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Related structure data

Related structure data	4zm5C 3b8pS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zm5-d 4e2h-d 3ry3-d 4bfb-d 2oxh-d 5m6a-d 4fmt-d 3do9-d 4lvn-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

82.9 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)	80.890, 61.310, 90.860
Angle α, β, γ (deg.)	90.00, 94.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chain length determinant protein / Polysaccharide antigen chain regulator Mass: 27566.908 Da / Num. of mol.: 3 / Fragment: UNP residues 54-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / 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-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.74 Å³/Da / Density % sol: 55.1 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 12.5mg/mL protein, 15% PEG400, 15% Peg 8000, 0.1M MgCl, pH 7.7 (0.1M Newman buffer Citric Acid:HEPES:CHES)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 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: 2.42→90.63 Å / Num. all: 32168 / Num. obs: 28733 / % possible obs: 93.7 % / Redundancy: 3.8 % / B_iso Wilson estimate: 52.88 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.42→2.51 Å / Redundancy: 3.3 % / R_merge(I) obs: 1.282 / Mean I/σ(I) obs: 0.9 / % possible all: 61

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Processing

Software

Name	Version	Classification
BUSTER	2.10.0	refinement
Coot	0.7	model building
PHENIX	2.4.0	phasing
XSCALE	July 4, 2012	data scaling
XDS	July 4, 2012	data reduction
Blu-Ice		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3B8P

3b8p

Resolution: 2.55→31.68 Å / Cor.coef. F_o:F_c: 0.9446 / Cor.coef. F_o:F_c free: 0.93 / SU R Cruickshank DPI: 0.487 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.447 / SU R_free Blow DPI: 0.248 / SU R_free Cruickshank DPI: 0.256

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2245	1430	4.98 %	RANDOM
R_work	0.1933	-	-	-
obs	0.1948	28725	98.26 %	-

Displacement parameters

B_iso mean: 69.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.6396 Å²	0 Å²	0.5648 Å²
2-	-	2.144 Å²	0 Å²
3-	-	-	5.4957 Å²

Refine analyze

Luzzati coordinate error obs: 0.404 Å

Refinement step

Cycle: 1 / Resolution: 2.55→31.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5633	0	15	58	5706

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	5724	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.09	7756	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2774	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		213	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		785	HARMONIC	5
X-RAY DIFFRACTION	t_it		5724	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	2.64
X-RAY DIFFRACTION	t_other_torsion	3.4
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		771	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		6635	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.55→2.65 Å / Total num. of bins used: 14

	R_factor	Num. reflection	% reflection
R_free	0.2514	146	5.01 %
R_work	0.2344	2767	-
all	0.2353	2913	-
obs	-	-	98.26 %

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	2.2907	0.1411	-1.8907	2.0828	1.199	6.3737	-0.1009	-0.2179	0.1417	0.2581	0.2201	0.0216	0.016	-0.0888	-0.1191	0.0101	0.0241	-0.0537	-0.2901	-0.0005	-0.3442	-15.4681	-17.2581	-37.494
2	-0.1366	-0.5285	1.032	0	3.2275	9.4642	0.0372	0.0134	0.0231	-0.0447	-0.0666	-0.1755	-0.4434	-0.5737	0.0294	0.5042	-0.1146	0.009	-0.1781	-0.0741	-0.1991	-20.9026	1.7641	-8.8689
3	0.3928	-1.8998	4.1374	15.2483	0.0228	8.8973	-0.1792	0.0131	0.482	0.4145	-0.1579	-0.1868	-1.1646	0.4722	0.3371	0.5131	0.067	-0.2	-0.2568	-0.0059	-0.2597	-16.4419	16.308	27.8726
4	0.5093	-3.2626	-3.7857	4.8403	6.5773	8.8608	0.08	-0.1502	0.1645	-0.0057	0.32	-0.4194	-0.7466	0.8488	-0.3999	0.5049	-0.2276	0.0316	-0.0479	-0.2398	-0.1133	-12.1978	3.1825	-13.7414
5	-0.9984	-0.7402	8.6427	0.1794	-1.4114	5.2584	-0.066	0.2396	-0.7298	-0.334	-0.011	0.1088	0.4146	-0.114	0.0769	0.3625	-0.075	-0.0025	-0.1386	-0.0742	-0.2062	-10.6907	-24.8866	-54.864
6	1.6994	-0.3171	-1.3039	2.3613	0.1244	4.607	-0.1698	0.417	-0.1723	-0.1588	0.2629	-0.1275	-0.0677	-0.4272	-0.0931	0.0184	-0.1126	-0.0362	-0.0532	-0.065	-0.3432	-32.6133	-21.5667	-22.4085
7	2.4508	0.2551	-0.2408	1.0316	-1.9753	7.2479	-0.2153	0.479	-0.0212	-0.2135	0.0072	0.2898	0.3093	-1.4429	0.2082	0.0697	-0.1643	-0.067	0.2286	-0.1498	-0.181	-35.7221	-24.0579	-32.3201
8	1.5531	1.6252	3.1752	1.9408	5.1946	10.8469	0.0448	0.0108	0.0542	-0.0245	-0.1415	-0.0505	0.6278	-0.5805	0.0967	0.1404	-0.0468	-0.0485	-0.0956	-0.039	-0.2512	-28.7348	-11.0176	10.0829
9	1.8767	-0.2971	1.9624	1.5461	-0.0196	7.5944	-0.2773	-0.0528	0.329	-0.0231	-0.0912	0.0946	-0.3986	-0.1201	0.3685	-0.0073	0.0451	-0.0294	-0.3253	-0.0048	-0.3042	-19.9665	2.9294	25.6919
10	2.4411	1.4675	4.0718	0	-4.997	4.4362	0.118	0.2305	0.104	0.3672	-0.1315	0.165	-0.4637	-0.688	0.0134	0.1371	0.0661	-0.0317	0.2464	-0.1023	-0.1533	-35.4043	-16.9132	-33.2067
11	1.2543	-0.6083	0.69	0	0.4737	10.7323	-0.3141	0.097	-0.2112	-0.0553	0.0177	0.1479	0.9095	-0.356	0.2965	0.1953	-0.2351	0.0302	-0.2471	-0.0666	-0.3145	-28.931	-36.2385	-10.487
12	2.2654	2.7325	3.9045	3.714	4.9139	8.5082	0.0549	0.3458	-0.3278	0.1076	0.3001	-0.317	0.884	0.4278	-0.355	0.2158	0.027	-0.015	-0.2501	-0.0419	-0.239	-16.5476	-26.5116	18.3725
13	5.2659	3.0644	1.976	5.1436	0.0897	2.0114	-0.1723	-0.1269	0.1599	0.1306	-0.0042	-0.0888	-0.4293	0.0609	0.1765	0.1464	0.0162	-0.0612	-0.1757	-0.0326	-0.2243	-4.0726	0.1063	42.8669
14	3.9163	-3.8516	1.8277	8.3542	-0.32	9.9219	-0.0906	0.2524	-0.1674	-0.3715	-0.0547	0.6137	0.2803	-0.4555	0.1453	0.1837	0.0583	-0.0495	-0.158	-0.0125	-0.2843	-23.3939	-20.4815	17.9701
15	6.1758	0.1438	3.4477	2.6851	-1.8822	0.4741	-0.2389	0.3338	-0.4791	0.226	0.3575	0.2572	0.5496	-1.2083	-0.1186	0.0714	-0.4561	0.0833	0.107	-0.1215	-0.3515	-38.83	-37.8635	-15.004

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|5 - 102 }
2	X-RAY DIFFRACTION	2	{ A\|103 - 152 }
3	X-RAY DIFFRACTION	3	{ A\|153 - 191 }
4	X-RAY DIFFRACTION	4	{ A\|192 - 232 }
5	X-RAY DIFFRACTION	5	{ A\|233 - 239 }
6	X-RAY DIFFRACTION	6	{ B\|3 - 70 }
7	X-RAY DIFFRACTION	7	{ B\|71 - 107 }
8	X-RAY DIFFRACTION	8	{ B\|108 - 151 }
9	X-RAY DIFFRACTION	9	{ B\|152 - 220 }
10	X-RAY DIFFRACTION	10	{ B\|221 - 240 }
11	X-RAY DIFFRACTION	11	{ C\|5 - 99 }
12	X-RAY DIFFRACTION	12	{ C\|100 - 152 }
13	X-RAY DIFFRACTION	13	{ C\|153 - 201 }
14	X-RAY DIFFRACTION	14	{ C\|202 - 222 }
15	X-RAY DIFFRACTION	15	{ C\|223 - 240 }

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