PDB-3u1d: The structure of a protein with a GntR superfamily winged-helix-t...

ID or keywords:

Entry

Database: PDB / ID: 3u1d

Title

The structure of a protein with a GntR superfamily winged-helix-turn-helix domain from Halomicrobium mukohataei.

Components

uncharacterized protein

Keywords

Structural Genomics / Unknown Function / GntR-superfamily / PSI-Biology / Midwest Center for Structural Genomics / MCSG / winged-helix-turn-helix / WHTH / putative DNA-binding

Function / homology

Helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / DI(HYDROXYETHYL)ETHER / ArsR family transcriptional regulator

Function and homology information

Biological species

Halomicrobium mukohataei (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Cuff, M.E. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a protein with a GntR superfamily winged-helix-turn-helix domain from Halomicrobium mukohataei.
Authors: Cuff, M.E. / Bigelow, L. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

-
Download

PDBx/mmCIF format	3u1d.cif.gz	141.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3u1d.ent.gz	110.3 KB	Display	PDB format
PDBx/mmJSON format	3u1d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3u1d_validation.pdf.gz	462.2 KB	Display	wwPDB validaton report
Full document	3u1d_full_validation.pdf.gz	463.8 KB	Display
Data in XML	3u1d_validation.xml.gz	19.2 KB	Display
Data in CIF	3u1d_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/3u1d ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1d	HTTPS FTP

-
Related structure data

Similar structure data	6w3s-2 5fpi-d 5xhx-2 6w3p-2 6w3o-2 4dwu-d 4gzg-d 6w3x-2 6w3y-1 5hno-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc101222

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein

B: uncharacterized protein

hetero molecules

35.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	57.214, 57.214, 218.354
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Details

likely the AB dimer in the AU.

-
Protein , 1 types, 2 molecules AB

#1: Protein	uncharacterized protein Mass: 17391.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomicrobium mukohataei (archaea) / Strain: DSM 12286 / Gene: Hmuk_3159 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C7P2E9

#1: Protein

uncharacterized protein

Mass: 17391.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Halomicrobium mukohataei (archaea) / Strain: DSM 12286 / Gene: Hmuk_3159 / Plasmid: pMCSG48 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C7P2E9

-
Non-polymers , 5 types, 300 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.11 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 0.1M Tris:HCl pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97912 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2011

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97912 Å / Relative weight: 1

Reflection

Redundancy: 14.1 % / Av σ(I) over netI: 44.44 / Number: 491614 / R_merge(I) obs: 0.082 / Χ²: 1.51 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 34958 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.88	50	98.4	1	0.062	4.463	12.2
3.88	4.88	100	1	0.055	3.14	13.2
3.39	3.88	100	1	0.067	3.354	13.6
3.08	3.39	100	1	0.076	2.832	13.8
2.86	3.08	100	1	0.079	2.101	14.1
2.69	2.86	100	1	0.083	1.673	14.2
2.55	2.69	100	1	0.093	1.459	14.3
2.44	2.55	100	1	0.098	1.248	14.2
2.35	2.44	100	1	0.111	1.138	14.3
2.27	2.35	100	1	0.12	1.048	14.4
2.2	2.27	100	1	0.146	0.964	14.3
2.13	2.2	100	1	0.157	0.89	14.4
2.08	2.13	100	1	0.199	0.827	14.3
2.03	2.08	100	1	0.244	0.763	14.4
1.98	2.03	100	1	0.285	0.738	14.3
1.94	1.98	100	1	0.37	0.775	14.5
1.9	1.94	100	1	0.41	0.74	14.3
1.86	1.9	100	1	0.537	0.726	14.4
1.83	1.86	100	1	0.66	0.715	14.4
1.8	1.83	100	1	0.869	0.785	14.2

Reflection

Resolution: 1.8→50 Å / Num. all: 34958 / Num. obs: 34958 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / R_merge(I) obs: 0.082 / Net I/σ(I): 7.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.8-1.83	14.2	0.869	1	100
1.83-1.86	14.4	0.66	1	100
1.86-1.9	14.4	0.537	1	100
1.9-1.94	14.3	0.41	1	100
1.94-1.98	14.5	0.37	1	100
1.98-2.03	14.3	0.285	1	100
2.03-2.08	14.4	0.244	1	100
2.08-2.13	14.3	0.199	1	100
2.13-2.2	14.4	0.157	1	100
2.2-2.27	14.3	0.146	1	100
2.27-2.35	14.4	0.12	1	100
2.35-2.44	14.3	0.111	1	100
2.44-2.55	14.2	0.098	1	100
2.55-2.69	14.3	0.093	1	100
2.69-2.86	14.2	0.083	1	100
2.86-3.08	14.1	0.079	1	100
3.08-3.39	13.8	0.076	1	100
3.39-3.88	13.6	0.067	1	100
3.88-4.88	13.2	0.055	1	100
4.88-50	12.2	0.062	1	98.4

-
Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2 Å / D res low: 50 Å / FOM : 0.301 / FOM acentric: 0.363 / FOM centric: 0 / Reflection: 25545 / Reflection acentric: 21178 / Reflection centric: 4367

Phasing MAD set

R cullis acentric: 1.67 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 21178 / Reflection centric: 4367

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
12.5-50	1.62	0.5	0.2	46	74
7.14-12.5	1.39	0.4	0.3	296	208
5-7.14	1.82	0.4	0.2	810	359
3.85-5	1.21	0.3	0.2	1544	482
3.13-3.85	1.28	0.2	0.1	2539	612
2.63-3.13	1.88	0.2	0.1	3775	752
2.27-2.63	2.15	0.1	0	5235	872
2-2.27	2.53	0.1	0	6933	1008

Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

ID	B iso	Fract x	Fract y	Fract z	Occupancy
1	32.5498	-0.151	-0.261	-0.091	4.501
2	35.1631	-0.098	-0.375	-0.022	4.367
3	40.5866	0.088	-0.511	0.043	4.683
4	43.1591	-0.34	-0.198	-0.161	4.055
5	46.9346	-0.02	-0.257	-0.111	2.345

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
12.5-50	0.192	0.501	120	46	74
7.14-12.5	0.318	0.541	504	296	208
5-7.14	0.391	0.565	1169	810	359
3.85-5	0.414	0.543	2026	1544	482
3.13-3.85	0.398	0.494	3151	2539	612
2.63-3.13	0.383	0.459	4527	3775	752
2.27-2.63	0.298	0.347	6107	5235	872
2-2.27	0.176	0.202	7941	6933	1008

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 34738

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.74-100	70.3	0.278	503
6.06-7.74	67.9	0.835	517
5.15-6.06	67.2	0.872	618
4.56-5.15	61.1	0.906	707
4.13-4.56	62.2	0.891	770
3.8-4.13	63.3	0.903	837
3.54-3.8	63.8	0.885	902
3.33-3.54	63.3	0.877	952
3.15-3.33	62.4	0.882	1009
3-3.15	64	0.872	1045
2.87-3	61.2	0.885	1090
2.75-2.87	62.3	0.882	1151
2.65-2.75	60	0.886	1203
2.55-2.65	65.8	0.884	1221
2.47-2.55	63	0.879	1269
2.4-2.47	65.3	0.889	1298
2.33-2.4	67.2	0.887	1348
2.26-2.33	67.3	0.891	1375
2.2-2.26	67.4	0.881	1398
2.15-2.2	68.8	0.886	1473
2.1-2.15	71.8	0.88	1466
2.05-2.1	71.1	0.891	1513
2.01-2.05	75.6	0.875	1560
1.97-2.01	88.3	0.886	1546
1.93-1.97	90.7	0.859	1603
1.89-1.93	91	0.856	1655
1.86-1.89	89.9	0.814	1657
1.8-1.86	90.8	0.645	3052

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.931 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1102 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19414	1745	5 %	RANDOM
R_work	0.17148	-	-	-
obs	0.17264	33030	99.88 %	-
all	-	34775	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 28.588 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.27 Å²	0 Å²	0 Å²
2-	-	-0.27 Å²	0 Å²
3-	-	-	0.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2348	0	40	289	2677

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	2470
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1730
X-RAY DIFFRACTION	r_angle_refined_deg	1.573	1.981	3349
X-RAY DIFFRACTION	r_angle_other_deg	0.957	3	4164
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.308	5	299
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.263	23.333	138
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.589	15	416
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.649	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	365
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2784
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	517
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	121	-
R_work	0.275	2126	-
obs	-	-	99.87 %

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	1.4293	1.1965	-0.8663	1.8958	-1.2457	1.4368	0.0325	-0.1303	-0.1118	0.1534	-0.1216	-0.1142	-0.0005	0.0647	0.0891	0.0541	0.0005	0.0097	0.0756	0.0711	0.0701	5.1432	21.176	50.2135
2	0.7661	0.1676	-0.4074	1.479	-0.6557	1.7144	0.0518	0.0018	0.1595	0.1577	-0.0372	0.0093	-0.1675	0.044	-0.0146	0.0289	-0.0158	-0.0075	0.084	0.0754	0.1029	11.5132	50.0111	31.7243

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 148
2	X-RAY DIFFRACTION	2	B	5 - 147

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 300 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 300 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 300 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi