PDB-4qif: Crystal Structure of PduA with edge mutation K26A and pore mutati...

ID or keywords:

Entry

Database: PDB / ID: 4qif

Title

Crystal Structure of PduA with edge mutation K26A and pore mutation S40H

Components

Propanediol utilization protein PduA

Keywords

STRUCTURAL PROTEIN /

BMC domain /

Potassium /

Glycerol / 1-2 propanediol /

tartaric acid /

sulfate ion

Function / homology

Function and homology information

propanediol degradation polyhedral organelle / propanediol catabolic process
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9951 Å

Authors

Pang, A.H. / Sawaya, M.R. / Yeates, T.O.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Selective molecular transport through the protein shell of a bacterial microcompartment organelle.
Authors: Chowdhury, C. / Chun, S. / Pang, A. / Sawaya, M.R. / Sinha, S. / Yeates, T.O. / Bobik, T.A.

History

Deposition	May 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Mar 11, 2015	Group: Database references
Revision 1.3	Mar 25, 2015	Group: Database references
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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	4qif.cif.gz	314 KB	Display	PDBx/mmCIF format
PDB format	pdb4qif.ent.gz	259 KB	Display	PDB format
PDBx/mmJSON format	4qif.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qi/4qif ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qif	HTTPS FTP

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Related structure data

Related structure data	4qigC 4rbtC 4rbuC 4rbvC 3ngk 4p2s 4ppd C: citing same article (ref.)
Similar structure data	4qie-1 4qig-1 2ewh-1 4p2s-2 4rbu-2 4p2s-1 4rbt-1 4rbv-1 4rbu-1 4rbv-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (7) #165 - Sep 2013 Designed Protein Cages similarity (4) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Propanediol utilization protein PduA

B: Propanediol utilization protein PduA

C: Propanediol utilization protein PduA

D: Propanediol utilization protein PduA

E: Propanediol utilization protein PduA

F: Propanediol utilization protein PduA

G: Propanediol utilization protein PduA

H: Propanediol utilization protein PduA

I: Propanediol utilization protein PduA

hetero molecules

98 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Propanediol utilization protein PduA

B: Propanediol utilization protein PduA

C: Propanediol utilization protein PduA

D: Propanediol utilization protein PduA

E: Propanediol utilization protein PduA

F: Propanediol utilization protein PduA

hetero molecules

defined by author&software
65.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Propanediol utilization protein PduA

H: Propanediol utilization protein PduA

I: Propanediol utilization protein PduA

hetero molecules

G: Propanediol utilization protein PduA

H: Propanediol utilization protein PduA

I: Propanediol utilization protein PduA

hetero molecules

defined by author&software
64.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.750, 108.750, 334.290
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

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Protein , 1 types, 9 molecules ABCDEFGHI

#1: Protein	Propanediol utilization protein PduA Mass: 10584.161 Da / Num. of mol.: 9 / Mutation: S40H, K26A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pduA, STM2038 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1C7

#1: Protein

Propanediol utilization protein PduA

Mass: 10584.161 Da / Num. of mol.: 9 / Mutation: S40H, K26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pduA, STM2038 / Plasmid: pET22b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1C7

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Non-polymers , 6 types, 328 molecules

#2: Chemical	ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₆
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 300 / 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 Å³/Da / Density % sol: 58.93 %
Crystal grow	Temperature: 298 K / pH: 9 Details: 0.2M Na/K tartrate, 2.2M Ammonium sulfate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2013
Radiation	Monochromator: CRYO-COOLED DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.995→94.19 Å / Num. obs: 80002 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 33.94 Å² / Net I/σ(I): 11.79
Reflection shell	Resolution: 1.995→2.05 Å / Mean I/σ(I) obs: 1.05 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX	(phaser-mr)	model building
PHENIX	(phenix.refine: dev_1555)	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	(PHASER-MR)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9951→94.18 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 21.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.218	7987	10 %
R_work	0.184	-	-
obs	0.187	79885	99.3 %
all	-	79885	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 46.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.9951→94.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5571	0	159	300	6030

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5803
X-RAY DIFFRACTION	f_angle_d	1.189	7874
X-RAY DIFFRACTION	f_dihedral_angle_d	11.405	2029
X-RAY DIFFRACTION	f_chiral_restr	0.05	983
X-RAY DIFFRACTION	f_plane_restr	0.006	1001

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 (%)
1.9951-2.0177	0.3266	215	0.3305	1934	X-RAY DIFFRACTION	81
2.0177-2.0415	0.3285	263	0.2932	2366	X-RAY DIFFRACTION	100
2.0415-2.0664	0.2998	262	0.2769	2359	X-RAY DIFFRACTION	100
2.0664-2.0925	0.2928	264	0.2781	2384	X-RAY DIFFRACTION	100
2.0925-2.1201	0.2823	262	0.2591	2351	X-RAY DIFFRACTION	100
2.1201-2.1491	0.2665	262	0.2472	2358	X-RAY DIFFRACTION	100
2.1491-2.1798	0.2965	266	0.2458	2398	X-RAY DIFFRACTION	100
2.1798-2.2124	0.2829	263	0.2427	2365	X-RAY DIFFRACTION	100
2.2124-2.2469	0.2763	261	0.2369	2351	X-RAY DIFFRACTION	100
2.2469-2.2838	0.271	265	0.2332	2386	X-RAY DIFFRACTION	100
2.2838-2.3232	0.295	265	0.2331	2382	X-RAY DIFFRACTION	100
2.3232-2.3654	0.2616	265	0.2154	2381	X-RAY DIFFRACTION	100
2.3654-2.4109	0.238	264	0.199	2380	X-RAY DIFFRACTION	100
2.4109-2.4601	0.2288	265	0.1897	2383	X-RAY DIFFRACTION	100
2.4601-2.5136	0.2313	266	0.1808	2393	X-RAY DIFFRACTION	100
2.5136-2.5721	0.2365	264	0.1888	2379	X-RAY DIFFRACTION	100
2.5721-2.6364	0.2243	265	0.1879	2379	X-RAY DIFFRACTION	100
2.6364-2.7077	0.2247	267	0.1826	2408	X-RAY DIFFRACTION	100
2.7077-2.7874	0.2101	269	0.182	2419	X-RAY DIFFRACTION	100
2.7874-2.8774	0.2357	265	0.1834	2384	X-RAY DIFFRACTION	100
2.8774-2.9802	0.2257	269	0.1797	2419	X-RAY DIFFRACTION	100
2.9802-3.0996	0.2123	268	0.1752	2417	X-RAY DIFFRACTION	100
3.0996-3.2406	0.2187	268	0.1879	2410	X-RAY DIFFRACTION	100
3.2406-3.4115	0.2145	271	0.1659	2444	X-RAY DIFFRACTION	100
3.4115-3.6252	0.189	272	0.1539	2447	X-RAY DIFFRACTION	100
3.6252-3.9051	0.1759	271	0.1506	2435	X-RAY DIFFRACTION	100
3.9051-4.2981	0.1638	273	0.1445	2454	X-RAY DIFFRACTION	100
4.2981-4.9201	0.1866	275	0.1432	2486	X-RAY DIFFRACTION	100
4.9201-6.1986	0.1971	281	0.1737	2528	X-RAY DIFFRACTION	100
6.1986-94.2853	0.2235	302	0.1976	2718	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	3.2739	1.0496	0.3062	1.9289	-0.4657	4.2198	0.1387	-0.5404	0.2298	0.1148	-0.0557	0.1137	-0.1194	-0.176	-0.0656	0.2235	-0.0305	0.0178	0.3562	-0.0048	0.3158	8.1015	-44.2336	18.0732
2	3.0072	1.5334	-0.2925	2.0865	-0.0418	1.6	-0.0455	0.0165	0.249	-0.0956	0.0176	0.1738	-0.1143	-0.0694	0.0211	0.2046	0.0076	0.0013	0.2316	-0.0055	0.248	35.9857	-27.5993	0.1277
3	3.5596	1.2295	0.3818	3.1672	-1.1708	4.1915	-0.3575	0.493	0.2135	-0.3985	0.3236	0.3522	-0.072	-0.1759	0.0605	0.3408	-0.1081	-0.0527	0.3308	0.0418	0.3244	8.9487	-43.8558	-18.5899
4	2.4188	1.5435	-1.2266	1.751	0.1583	3.2043	-0.3289	0.5396	0.237	-0.5076	0.3418	0.3415	0.0459	-0.3743	-0.0235	0.3156	-0.0976	-0.0797	0.3163	0.0798	0.3119	27.375	-33.5474	-18.2221
5	3.9326	2.1389	-0.0826	1.7404	-0.5064	2.0726	-0.0756	0.0135	0.3527	-0.0727	0.1003	0.2195	-0.1467	-0.0647	-0.0241	0.2259	-0.0063	-0.0233	0.1658	0.0276	0.2677	-1.1504	-49.7235	-0.7695
6	3.2911	0.1776	0.0228	2.6162	0.8537	4.5106	0.1263	-0.2719	0.3861	0.0304	-0.0781	0.092	-0.3896	0.067	-0.0115	0.1659	-0.0248	0.0368	0.207	-0.0208	0.2006	25.9576	-33.0937	18.1227
7	1.4043	0.238	0.5255	3.1377	-0.8517	3.1518	-0.0066	0.1705	-0.0511	-0.4902	0.0448	-0.1629	0.1386	0.12	-0.0588	0.3069	0.0042	0.0515	0.2098	-0.0158	0.2798	58.125	-11.5142	-18.5784
8	1.0482	-0.3697	-0.6468	3.3613	-0.5523	3.5316	-0.0358	-0.1313	-0.1074	0.2572	0.0756	-0.2615	0.2114	0.2194	-0.0462	0.2861	0.0279	-0.065	0.283	0.0087	0.2641	58.9375	-10.7498	18.8849
9	1.337	0.4608	0.4162	3.4675	0.3161	2.7657	0.0703	0.0113	-0.2016	-0.0214	-0.0093	-0.3354	0.2313	0.2637	-0.0838	0.1976	0.017	-0.0168	0.2101	-0.002	0.246	58.8908	-21.1074	0.7243

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq -10:9999)
2	X-RAY DIFFRACTION	2	(chain B and resseq -10:9999)
3	X-RAY DIFFRACTION	3	(chain C and resseq -10:9999)
4	X-RAY DIFFRACTION	4	(chain D and resseq -10:9999)
5	X-RAY DIFFRACTION	5	(chain E and resseq -10:9999)
6	X-RAY DIFFRACTION	6	(chain F and resseq -10:9999)
7	X-RAY DIFFRACTION	7	(chain G and resseq -10:9999)
8	X-RAY DIFFRACTION	8	(chain H and resseq -10:9999)
9	X-RAY DIFFRACTION	9	(chain I and resseq -10:9999)

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