PDB-3hrt: Crystal Structure of ScaR with bound Cd2+

ID or keywords:

Entry

Database: PDB / ID: 3hrt

Title

Crystal Structure of ScaR with bound Cd2+

Components

Metalloregulator ScaR

Keywords

TRANSCRIPTION / DtxR/MntR family member

Function / homology

Function and homology information

transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function

Biological species

Streptococcus gordonii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Stoll, K.E. / Draper, W.E. / Kliegman, J.I. / Golynskiy, M.V. / Brew-Appiah, R.A.T. / Brown, H.K. / Breyer, W.A. / Jakubovics, N.S. / Jenkinson, H.F. / Brennan, R.B. ...

Citation

Journal: Biochemistry / Year: 2009
Title: Characterization and structure of the manganese-responsive transcriptional regulator ScaR.
Authors: Stoll, K.E. / Draper, W.E. / Kliegman, J.I. / Golynskiy, M.V. / Brew-Appiah, R.A. / Phillips, R.K. / Brown, H.K. / Breyer, W.A. / Jakubovics, N.S. / Jenkinson, H.F. / Brennan, R.G. / Cohen, S.M. / Glasfeld, A.

History

Deposition	Jun 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 23, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 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 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3hrt.cif.gz	185.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3hrt.ent.gz	151.1 KB	Display	PDB format
PDBx/mmJSON format	3hrt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3hrt_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	3hrt_full_validation.pdf.gz	466.3 KB	Display
Data in XML	3hrt_validation.xml.gz	18.4 KB	Display
Data in CIF	3hrt_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/3hrt ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hrt	HTTPS FTP

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Related structure data

Related structure data	3hrsSC 3hruC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3hrs-d 3hru-d 6o5c-1 5x18-d 1mm9-1 3jsb-2 3ew1-4 2c82-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: Metalloregulator ScaR

B: Metalloregulator ScaR

hetero molecules

49.8 kDa, 2 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)	70.860, 70.860, 304.100
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Metalloregulator ScaR Mass: 24701.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: scaR / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RFN3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.84 Å³/Da / Density % sol: 67.99 %
Crystal grow	Temperature: 298 K / Method: hanging drop / pH: 6 Details: 1.6 M lithium sulfate, 0.05 M sodium cacodylate in the presence of 1 mM MnCl2 and 1 mM duplex DNA, pH 6.0, hanging drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1.0781 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2006

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0781 Å / Relative weight: 1

Reflection

Resolution: 2.8→30.25 Å / Num. obs: 18587 / % possible obs: 92.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.084 / R_sym value: 0.084 / Net I/σ(I): 4.251

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.8-2.95	1.9	0.311	2.4	4234	2187	0.311	77.3
2.95-3.13	2.6	0.179	3.6	6192	2373	0.179	89.9
3.13-3.35	3.6	0.121	4.7	8920	2506	0.121	97.6
3.35-3.61	4.2	0.118	4.6	9870	2336	0.118	98.2
3.61-3.96	4.4	0.094	6.2	9529	2174	0.094	97.7
3.96-4.43	4.4	0.09	6.1	8739	1970	0.09	97.7
4.43-5.11	4.5	0.084	6.6	7922	1749	0.084	97.1
5.11-6.26	4.5	0.084	6.1	6749	1499	0.084	97
6.26-8.85	4.4	0.072	6.4	5168	1185	0.072	94.9
8.85-30.61	3.8	0.075	6.6	2304	608	0.075	82.2

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.5	data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3HRS

3hrs

Resolution: 2.8→30.25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.704 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.282	1809	9.8 %
R_work	0.23	-	-
obs	-	18453	92.01 %

Solvent computation

B_sol: 55.977 Å² / k_sol: 0.253 e/Å³

Displacement parameters

B_iso max: 293.96 Å² / B_iso mean: 127.411 Å² / B_iso min: 51.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.366 Å²	0 Å²	-0 Å²
2-	-	15.366 Å²	0 Å²
3-	-	-	-30.733 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→30.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3399	0	12	0	3411

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	1.201	1
X-RAY DIFFRACTION	f_bond_d	0.008	1
X-RAY DIFFRACTION	f_chiral_restr	0.078	1
X-RAY DIFFRACTION	f_dihedral_angle_d	21.389	1
X-RAY DIFFRACTION	f_plane_restr	0.005	1
X-RAY DIFFRACTION	f_nbd_refined	4.111	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.8-2.829	0.337	395	X-RAY DIFFRACTION	33	65
2.829-2.859	0.346	379	X-RAY DIFFRACTION	33	66
2.859-2.89	0.368	380	X-RAY DIFFRACTION	33	66
2.89-2.923	0.369	425	X-RAY DIFFRACTION	33	72
2.923-2.957	0.348	459	X-RAY DIFFRACTION	33	73
2.957-2.993	0.368	437	X-RAY DIFFRACTION	33	77
2.993-3.031	0.307	458	X-RAY DIFFRACTION	33	78
3.031-3.071	0.328	487	X-RAY DIFFRACTION	33	81
3.071-3.113	0.314	494	X-RAY DIFFRACTION	33	82
3.113-3.157	0.322	489	X-RAY DIFFRACTION	33	86
3.157-3.204	0.332	542	X-RAY DIFFRACTION	33	88
3.204-3.254	0.274	499	X-RAY DIFFRACTION	33	85
3.254-3.307	0.273	513	X-RAY DIFFRACTION	33	88
3.307-3.364	0.263	537	X-RAY DIFFRACTION	33	87
3.364-3.424	0.275	519	X-RAY DIFFRACTION	33	89
3.424-3.49	0.265	518	X-RAY DIFFRACTION	33	88
3.49-3.561	0.279	546	X-RAY DIFFRACTION	33	88
3.561-3.638	0.23	531	X-RAY DIFFRACTION	33	91
3.638-3.722	0.226	553	X-RAY DIFFRACTION	33	90
3.722-3.814	0.218	532	X-RAY DIFFRACTION	33	90
3.814-3.917	0.205	521	X-RAY DIFFRACTION	33	87
3.917-4.031	0.236	516	X-RAY DIFFRACTION	33	86
4.031-4.16	0.216	563	X-RAY DIFFRACTION	33	90
4.16-4.307	0.193	510	X-RAY DIFFRACTION	33	87
4.307-4.477	0.182	535	X-RAY DIFFRACTION	33	86
4.477-4.679	0.184	541	X-RAY DIFFRACTION	33	88
4.679-4.922	0.181	537	X-RAY DIFFRACTION	33	88
4.922-5.225	0.193	538	X-RAY DIFFRACTION	33	86
5.225-5.62	0.223	546	X-RAY DIFFRACTION	33	87
5.62-6.17	0.224	520	X-RAY DIFFRACTION	33	84
6.17-7.027	0.239	553	X-RAY DIFFRACTION	33	85
7.027-8.725	0.209	537	X-RAY DIFFRACTION	33	82
8.725-19.792	0.187	534	X-RAY DIFFRACTION	33	75

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	3.3399	1.125	1.2436	1.8415	-1.757	1.2183	0.6466	-0.2761	-0.2259	0.1558	-0.5913	-0.1911	0.2635	0.562	-0.0004	1.0412	0.1612	-0.0661	0.3245	0.0122	0.6782	-5.1948	43.0818	47.4677
2	1.5472	1.7222	-1.2274	0.2583	0.1183	1.5244	0.3695	0.0685	0.7073	0.1506	0.2381	0.8331	0.9563	0.911	-0.0001	2.4496	-0.2073	0.4326	1.0927	-0.0965	1.0709	7.3523	27.8185	3.0842
3	0.858	-1.1568	0.5225	-0.3198	-0.0619	0.4066	0.342	-0.1383	-0.3547	-1.1339	0.8334	-0.0888	-1.6034	1.3068	0.0007	2.0586	-0.16	0.4566	1.0699	-0.2714	1.1621	5.7187	17.6607	2.8365
4	2.223	-0.4124	0.4606	2.591	2.3913	6.1114	0.0331	-0.1194	0.2384	0.0793	-0.1113	0.1253	-0.864	-0.0383	0.0005	1.1164	0.03	0.0948	0.221	0.0256	0.7312	-15.2409	25.8712	35.6149
5	1.7489	-0.3233	-1.0407	1.6442	0.3969	3.2277	0.2189	0.72	-0.1828	-1.3366	-0.0779	0.1431	-0.163	0.4086	0.0003	1.699	0.1883	0.1008	0.3974	-0.0016	0.7074	-12.0455	19.8135	15.9926
6	3.8055	0.1139	-0.1801	1.4505	-0.4327	2.4241	0.3743	-1.5929	-0.2475	0.1137	0.2173	-0.155	0.0575	0.2368	-0.0012	1.4562	-0.1835	-0.1967	1.1422	0.1437	0.9943	-11.2008	17.6732	58.4959
7	0.5017	0.0603	0.6629	2.3168	0.2682	1.5512	0.2443	0.7903	0.1961	0.1482	-0.3023	-0.2838	-0.3286	0.1995	-0.0001	1.877	0.1347	0.1067	1.3165	0.1733	0.9337	-20.2835	25.5806	-6.3577

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and (resseq 3:70)	A	3 - 70
2	X-RAY DIFFRACTION	2	chain B and (resseq 6:52)	B	6 - 52
3	X-RAY DIFFRACTION	3	chain B and (resseq 53:72)	B	53 - 72
4	X-RAY DIFFRACTION	4	chain A and (resseq 71:138 or resseq 501)	A	71 - 138
5	X-RAY DIFFRACTION	4	chain A and (resseq 71:138 or resseq 501)	A	501
6	X-RAY DIFFRACTION	5	chain B and (resseq 73:140 or resseq 501)	B	73 - 140
7	X-RAY DIFFRACTION	5	chain B and (resseq 73:140 or resseq 501)	B	501
8	X-RAY DIFFRACTION	6	chain A and (resseq 139:215)	A	139 - 215
9	X-RAY DIFFRACTION	7	chain B and (resseq 141:214)	B	141 - 214

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