PDB-7ejg: Crystal structure of PBP domain of RMCA

ID or keywords:

Entry

Database: PDB / ID: 7ejg

Title

Crystal structure of PBP domain of RMCA

Components

EAL domain-containing protein

Keywords

PEPTIDE BINDING PROTEIN / Arginine receptor

Function / homology

Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / :

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.68 Å

Authors

Gu, L. / Li, N.

Citation

Journal: To Be Published
Title: Crystal structure of PBP domain of RMCA
Authors: Gu, L. / Li, N.

History

Deposition	Apr 2, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ejg.cif.gz	128.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7ejg.ent.gz	88.1 KB	Display	PDB format
PDBx/mmJSON format	7ejg.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/ej/7ejg ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ejg	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

Deposited unit

C: EAL domain-containing protein

hetero molecules

26.5 kDa, 1 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)	109.330, 109.330, 41.533
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁
Space group name Hall	P6₁
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: -x,-y,z+1/2

#1: Protein	EAL domain-containing protein Mass: 26270.113 Da / Num. of mol.: 1 / Fragment: UNP residues 26-259 / Mutation: L49K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: H5409_03030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G7AIH9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.62 Å³/Da / Density % sol: 53.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2%PEG550, 1.8M Ammonium sulfate, 0.1M BIS-TRIS hydrochloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0332 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.68→27.11 Å / Num. obs: 32306 / % possible obs: 99.23 % / Redundancy: 10.4 % / B_iso Wilson estimate: 32.25 Å² / CC_1/2: 1 / Net I/σ(I): 3.07
Reflection shell	Resolution: 1.68→1.74 Å / Num. unique obs: 3200 / CC_1/2: 0.916

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	model building
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX	1.16_3549	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.68→27.11 Å / SU ML: 0.2024 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2228	2002	6.2 %
R_work	0.1974	30304	-
obs	0.199	32306	99.19 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→27.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1854	0	12	132	1998

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1961
X-RAY DIFFRACTION	f_angle_d	1.1046	2680
X-RAY DIFFRACTION	f_chiral_restr	0.0673	296
X-RAY DIFFRACTION	f_plane_restr	0.0089	351
X-RAY DIFFRACTION	f_dihedral_angle_d	23.3414	739

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 (%)
1.68-1.72	0.3135	144	0.2575	2124	X-RAY DIFFRACTION	97.34
1.72-1.77	0.2869	144	0.2487	2144	X-RAY DIFFRACTION	99.96
1.77-1.82	0.2951	143	0.2441	2166	X-RAY DIFFRACTION	100
1.82-1.88	0.2863	141	0.2565	2179	X-RAY DIFFRACTION	100
1.88-1.95	0.3118	141	0.245	2141	X-RAY DIFFRACTION	100
1.95-2.03	0.241	142	0.2433	2182	X-RAY DIFFRACTION	100
2.03-2.12	0.2636	147	0.235	2168	X-RAY DIFFRACTION	100
2.12-2.23	0.26	146	0.2313	2171	X-RAY DIFFRACTION	100
2.23-2.37	0.2379	141	0.2157	2178	X-RAY DIFFRACTION	99.91
2.37-2.55	0.2271	144	0.2098	2187	X-RAY DIFFRACTION	100
2.55-2.81	0.2165	143	0.2035	2183	X-RAY DIFFRACTION	100
2.81-3.21	0.2296	149	0.1983	2185	X-RAY DIFFRACTION	100
3.21-4.05	0.2048	143	0.1679	2214	X-RAY DIFFRACTION	99.79
4.05-27.11	0.1899	134	0.1769	2082	X-RAY DIFFRACTION	91.91

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	0.0886323239577	-0.0536472314694	-0.142718868187	0.146287254261	0.0722389298009	0.242707945656	0.00652594861508	-0.311104126561	-0.0026196166977	-0.468354748417	-0.535090400311	0.160534968554	-0.439526142821	-0.430644008722	-0.67068093501	0.659801803191	0.357067930807	-0.17742223741	0.704850625561	-0.131443996836	-0.397780679858	-34.5527896472	49.5475567269	0.279399707735
2	0.223854458022	0.227241822787	0.147570114441	0.391414687548	0.0361251982875	0.0449977373024	0.0496389589672	0.498668830559	-0.080873307873	-0.00711641197552	-0.109053060807	-0.447214901816	-0.0778637700535	0.00856205456083	0.0178795701348	0.347193330301	0.0586815698155	0.0410917711165	0.404157089654	0.00697028393731	0.309176708404	-15.7900551523	40.0225105226	-6.03252319125
3	0.0961640591759	0.0141934170266	0.147915141069	0.0869172784612	0.0364050154664	0.174224163631	0.340996395725	0.540495964107	-0.128012872478	-0.417208141865	-0.279573680247	0.0561591893249	-0.00627656368258	-0.0193214080719	0.00129387785275	0.406201588518	0.0759801476954	0.00706540204817	0.456027105503	-0.0690690505244	0.262307773525	-20.8399350197	35.8234510038	-9.83583473625
4	0.217326821415	-0.201340990638	0.0646649576468	1.1841642964	-0.0686705024482	-0.0138324536537	0.158296741403	0.602498514506	0.524380726286	-0.25630955573	-0.263726109287	-0.492470507876	0.0261796913868	-0.0537246775236	0.022604363409	0.305106905783	0.0490028925953	0.0594400898504	0.402102295913	0.112010599332	0.366665118424	-11.9042550486	46.0291715268	-5.27792056855
5	0.267234532311	-0.198630515168	-0.125677061807	0.346373256896	0.0299862226359	0.0309528166764	0.0215385744372	-0.122558787196	0.0204706407308	0.0400694452941	0.087552951465	-0.313545605616	-0.0613848650827	-0.164443384186	0.00358519418463	0.316337688665	0.0367516961694	-0.0302645158342	0.326196758265	-0.0199331638786	0.248486536734	-15.5511675756	44.1999860595	4.78973665444
6	0.380723766126	-0.115274494869	0.00913882351418	0.410805158708	0.684032992709	1.09533014029	-0.106595865961	-0.222952499659	-0.429187217907	0.0266809639927	-0.4000961381	-0.75259675518	0.313646901718	0.141156684602	-0.740499872169	0.312910268132	0.0375619667161	-0.0418531592254	0.327047572463	0.371994108409	1.00852209871	-2.2669949388	21.9109723897	8.33266814244
7	0.112336662289	-0.218861736304	-0.282483673435	0.397593247701	0.535202668002	0.716466791311	0.135988404984	-0.332194156078	-0.322120274322	-0.0130107088508	0.0760996084208	-0.722393404568	-0.214210641146	0.26501333496	0.19543310175	0.179473283062	-0.0271466324532	-0.142234444234	0.577760276975	0.153726343594	0.764914741049	2.17101143771	30.9947350884	9.13283213496
8	0.0288131549129	-0.075241484169	-0.000521654417768	0.461433357463	-0.111862122456	0.0509648861943	0.0746184891249	-0.621097852732	-0.165636145129	0.184136493827	-0.0878316049087	-0.999880070801	0.0145756960044	0.0862196611413	0.00285528424023	0.270544126417	-0.0750517138705	-0.178565985086	0.605602776461	0.169177500216	0.719304109744	0.268900950527	35.6122211612	10.0085955924
9	0.558804237156	-0.116264050396	-0.485769213111	0.237199127633	0.528903000937	1.34963772189	0.046394253577	0.0318621503116	-0.862420775082	-0.267700954703	-0.477825401016	-0.97954377531	0.405642419103	0.0293711712252	-0.536996189275	0.27109979842	0.0821406736247	0.0542822066337	0.293395278431	0.0955228406818	0.968365186658	-1.72916212859	23.2430512104	-0.46601105658
10	0.883982649154	0.102388337433	-0.085704086833	0.162154240453	0.0554601186836	0.188433759621	-0.0267290049761	-0.243336078547	-0.267624604854	0.192396887602	0.0733192438422	-0.119825638774	-0.167807748862	-0.103881859691	-0.0103419671604	0.267688464201	0.027463808439	-0.0312930928827	0.322661201387	0.0282215005247	0.199230004199	-21.9076766009	39.5341318631	6.10076686015
11	0.00338639488342	0.0130948590423	-0.0128825437991	0.0199989111451	-0.0026608011627	0.0420450011944	-0.0806879441364	-0.324545895127	-0.573717359318	-0.198334615878	0.115286710494	0.149733760882	0.259681461211	-0.0877172823848	0.00026490099886	0.397386042249	-0.000427486132236	-0.0641809383167	0.368153602344	-0.123488241449	0.842983573836	-23.3801288534	23.1375825923	-3.59934747132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid -1 through 10 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 11 through 26 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 27 through 49 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 50 through 69 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 70 through 95 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 96 through 114 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 115 through 128 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 129 through 148 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 149 through 188 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 189 through 218 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 219 through 234 )

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