PDB-3hru: Crystal Structure of ScaR with bound Zn2+

ID or keywords:

Entry

Database: PDB / ID: 3hru

Title

Crystal Structure of ScaR with bound Zn2+

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: 2.9 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	3hru.cif.gz	183.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3hru.ent.gz	150.3 KB	Display	PDB format
PDBx/mmJSON format	3hru.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/3hru ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hru	HTTPS FTP

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Related structure data

Related structure data	3hrsSC 3hrtC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6o5c-1 3hrs-d 3hrt-d 1mm9-1 5joc-d 5edk-d 6wl2-3 2fv7-d 2qyk-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

49.9 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)	70.700, 70.700, 301.900
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-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.8 Å³/Da / Density % sol: 67.61 %
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: 4.2.2 / Wavelength: 1.2131 Å

Detector

Type: NOIR-1 / Detector: CCD / Date: Feb 11, 2006

Radiation

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

Radiation wavelength

Wavelength: 1.2131 Å / Relative weight: 1

Reflection

Resolution: 2.9→49.99 Å / Num. obs: 17514 / % possible obs: 96.9 % / Redundancy: 6.17 % / R_merge(I) obs: 0.071 / Χ²: 0.96 / Scaling rejects: 817

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
2.9-3	4.28	0.449	2	5977	1389	1.3	79.2
3-3.12	4.73	0.362	2.8	7723	1621	1.3	92.1
3.12-3.27	5.83	0.291	3.8	10171	1726	1.19	99
3.27-3.44	6.52	0.194	5.8	11694	1773	1.15	99.9
3.44-3.65	6.84	0.141	8.2	12151	1754	1.22	100
3.65-3.94	6.66	0.125	8.9	12199	1802	1.2	100
3.94-4.33	6.74	0.074	12.9	11996	1777	0.66	99.9
4.33-4.96	6.66	0.063	15.4	12179	1822	0.66	99.9
4.96-6.24	6.65	0.058	16.8	12394	1858	0.64	100
6.24-49.99	6.18	0.04	21.7	12359	1992	0.7	98.4

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Processing

Software

Name	Version	Classification
d*TREK	9.4LDz	data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
d*TREK		data reduction
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3HRS

3hrs

Resolution: 2.9→49.99 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.73 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.292	1713	9.94 %
R_work	0.23	-	-
obs	-	17233	96.22 %

Solvent computation

B_sol: 40.727 Å² / k_sol: 0.258 e/Å³

Displacement parameters

B_iso max: 214.83 Å² / B_iso mean: 106.754 Å² / B_iso min: 37.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.862 Å²	0 Å²	-0 Å²
2-	-	6.862 Å²	0 Å²
3-	-	-	-13.724 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→49.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3350	0	22	4	3376

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	1.411	1
X-RAY DIFFRACTION	f_bond_d	0.01	1
X-RAY DIFFRACTION	f_chiral_restr	0.088	1
X-RAY DIFFRACTION	f_dihedral_angle_d	22.258	1
X-RAY DIFFRACTION	f_plane_restr	0.004	1
X-RAY DIFFRACTION	f_nbd_refined	4.117	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.9-2.932	0.337	370	X-RAY DIFFRACTION	31	63
2.932-2.965	0.341	388	X-RAY DIFFRACTION	31	71
2.965-3	0.331	426	X-RAY DIFFRACTION	31	77
3-3.037	0.338	436	X-RAY DIFFRACTION	31	76
3.037-3.075	0.358	446	X-RAY DIFFRACTION	31	78
3.075-3.115	0.336	464	X-RAY DIFFRACTION	31	86
3.115-3.158	0.312	488	X-RAY DIFFRACTION	31	87
3.158-3.203	0.321	511	X-RAY DIFFRACTION	31	90
3.203-3.25	0.294	495	X-RAY DIFFRACTION	31	89
3.25-3.301	0.27	506	X-RAY DIFFRACTION	31	90
3.301-3.355	0.263	525	X-RAY DIFFRACTION	31	90
3.355-3.412	0.273	491	X-RAY DIFFRACTION	31	90
3.412-3.474	0.265	501	X-RAY DIFFRACTION	31	89
3.474-3.54	0.27	514	X-RAY DIFFRACTION	31	88
3.54-3.612	0.242	490	X-RAY DIFFRACTION	31	88
3.612-3.69	0.206	508	X-RAY DIFFRACTION	31	89
3.69-3.776	0.222	498	X-RAY DIFFRACTION	31	88
3.776-3.869	0.213	520	X-RAY DIFFRACTION	31	90
3.869-3.973	0.225	522	X-RAY DIFFRACTION	31	90
3.973-4.089	0.201	500	X-RAY DIFFRACTION	31	90
4.089-4.22	0.189	531	X-RAY DIFFRACTION	31	90
4.22-4.369	0.17	521	X-RAY DIFFRACTION	31	91
4.369-4.542	0.155	524	X-RAY DIFFRACTION	31	90
4.542-4.747	0.175	532	X-RAY DIFFRACTION	31	90
4.747-4.993	0.17	529	X-RAY DIFFRACTION	31	91
4.993-5.3	0.188	527	X-RAY DIFFRACTION	31	91
5.3-5.701	0.247	524	X-RAY DIFFRACTION	31	89
5.701-6.259	0.218	537	X-RAY DIFFRACTION	31	88
6.259-7.128	0.265	549	X-RAY DIFFRACTION	31	90
7.128-8.849	0.214	555	X-RAY DIFFRACTION	31	89
8.849-19.99	0.198	592	X-RAY DIFFRACTION	31	89

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	1.0856	1.1173	-0.3319	3.6692	0.7125	1.4164	0.183	0.4238	0.0179	-0.4158	-0.2443	0.5781	0.3306	-0.2564	-0.0003	0.8619	-0.1313	-0.0829	0.2594	0.013	0.6608	76.0681	113.6227	28.6221
2	2.2556	0.4101	-0.6329	1.6819	-1.7692	3.8015	0.0866	0.0595	0.1823	0.0176	0.0451	0.0347	-0.4967	0.2017	-0.0002	0.7601	-0.0304	0.0932	0.1131	-0.0196	0.5624	86.0678	96.3675	39.4608
3	4.636	1.745	-0.8644	2.574	0.1626	2.9918	0.9789	1.5938	-0.5207	0.2419	-0.083	0.3075	0.1158	-0.3172	-0.0025	1.158	0.2724	-0.2544	0.6923	-0.1449	0.6887	81.7037	88.3927	16.8124
4	-0.0845	0.0481	-0.089	-0.1036	0.0125	0.295	0.003	-0.9916	0.8945	-0.6211	0.8495	-0.3206	-0.5883	0.3856	-0.0006	2.0935	0.0516	0.5477	0.7848	-0.0016	0.8164	68.6467	95.9205	69.6616
5	-0.1977	-0.7146	-0.0198	-0.1901	0.6526	0.4521	-0.3095	-0.1879	0.5776	0.1974	0.4708	-0.5145	-0.6227	0.0133	-0.0011	2.0505	-0.0341	0.0856	1.0729	0.032	1.3804	62.4634	98.6626	73.6996
6	1.0979	-0.0701	-0.098	-0.6113	-0.5447	1.9924	0.7102	-0.6565	0.1108	0.9554	-0.2272	-0.1549	-0.5906	-0.188	0.0001	1.3742	-0.1498	0.176	0.4587	-0.0506	0.6572	76.1204	92.6029	64.8776
7	0.8113	1.8125	-1.3146	1.0238	-0.5104	2.1398	0.4579	-0.6782	0.113	0.4391	-0.376	0.1153	0.7632	-0.2226	0.0012	1.2987	-0.24	0.0804	0.4957	0.0051	0.6232	80.5035	86.8405	59.4883
8	1.3783	0.1056	1.1032	3.0835	-1.0587	1.0635	0.2159	-0.7899	0.3298	0.6195	-0.0349	0.4282	-0.375	-0.085	-0.0003	1.1846	-0.2018	0.0942	1.2141	-0.2104	0.7168	90.7033	96.1244	81.5612

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 resid 3:70)	A	3 - 70
2	X-RAY DIFFRACTION	2	(chain A and resid 71:140)	A	71 - 140
3	X-RAY DIFFRACTION	3	(chain A and resid 141:215)	A	141 - 215
4	X-RAY DIFFRACTION	4	(chain B and resid 6:15)	B	6 - 15
5	X-RAY DIFFRACTION	5	(chain B and resid 16:49)	B	16 - 49
6	X-RAY DIFFRACTION	6	(chain B and resid 50:97)	B	50 - 97
7	X-RAY DIFFRACTION	7	(chain B and resid 98:140)	B	98 - 140
8	X-RAY DIFFRACTION	8	(chain B and resid 141:215)	B	141 - 215

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