PDB-3aqd: Unliganded TRAP

ID or keywords:

Entry

Database: PDB / ID: 3aqd

Title

Unliganded TRAP

Components

Transcription attenuation protein mtrB

Keywords

RNA BINDING PROTEIN / 11-fold symmetric ring / Control of tryptophan synthesis / Tryptophan and Anti-TRAP

Function / homology

Function and homology information

DNA-templated transcription termination / regulation of DNA-templated transcription /

RNA binding / identical protein binding
Similarity search - Function

Biological species

Bacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Malay, A.A.D. / Watanabe, M. / Heddle, J.G. / Tame, J.R.H.

Citation

Journal: To be Published
Title: Allostery in TRAP
Authors: Malay, A.A.D. / Watanabe, M. / Heddle, J.G. / Tame, J.R.H.

History

Deposition	Oct 29, 2010	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3aqd.cif.gz	538.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3aqd.ent.gz	451.8 KB	Display	PDB format
PDBx/mmJSON format	3aqd.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/aq/3aqd ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aqd	HTTPS FTP

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Related structure data

Related structure data	1qawS 1c9s 1gtf 1gtn 1utd 2exs 2ext 2zcz 2zd0 2zp8 2zp9 4v4f S: Starting model for refinement
Similar structure data	5ef2-1 1utd-1 5eeu-1 5eez-1 1wap-1 5eev-1 1gtf-1 4v4f-4 1gtn-1 5eey-1 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

Deposited unit

A: Transcription attenuation protein mtrB

B: Transcription attenuation protein mtrB

C: Transcription attenuation protein mtrB

D: Transcription attenuation protein mtrB

E: Transcription attenuation protein mtrB

F: Transcription attenuation protein mtrB

G: Transcription attenuation protein mtrB

H: Transcription attenuation protein mtrB

I: Transcription attenuation protein mtrB

J: Transcription attenuation protein mtrB

K: Transcription attenuation protein mtrB

L: Transcription attenuation protein mtrB

M: Transcription attenuation protein mtrB

N: Transcription attenuation protein mtrB

O: Transcription attenuation protein mtrB

P: Transcription attenuation protein mtrB

Q: Transcription attenuation protein mtrB

R: Transcription attenuation protein mtrB

S: Transcription attenuation protein mtrB

T: Transcription attenuation protein mtrB

U: Transcription attenuation protein mtrB

V: Transcription attenuation protein mtrB

182 kDa, 22 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcription attenuation protein mtrB

B: Transcription attenuation protein mtrB

C: Transcription attenuation protein mtrB

D: Transcription attenuation protein mtrB

E: Transcription attenuation protein mtrB

F: Transcription attenuation protein mtrB

G: Transcription attenuation protein mtrB

H: Transcription attenuation protein mtrB

I: Transcription attenuation protein mtrB

J: Transcription attenuation protein mtrB

K: Transcription attenuation protein mtrB

defined by author&software
90.8 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

L: Transcription attenuation protein mtrB

M: Transcription attenuation protein mtrB

N: Transcription attenuation protein mtrB

O: Transcription attenuation protein mtrB

P: Transcription attenuation protein mtrB

Q: Transcription attenuation protein mtrB

R: Transcription attenuation protein mtrB

S: Transcription attenuation protein mtrB

T: Transcription attenuation protein mtrB

U: Transcription attenuation protein mtrB

V: Transcription attenuation protein mtrB

defined by author&software
90.8 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.154, 85.432, 127.444
Angle α, β, γ (deg.)	90.00, 95.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 2

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	SER	SER	LYS	LYS	A	A	7 - 75	5 - 73
2	SER	SER	LYS	LYS	B	B	7 - 75	5 - 73
3	SER	SER	GLY	GLY	C	C	7 - 74	5 - 72
4	SER	SER	GLY	GLY	D	D	7 - 74	5 - 72
5	SER	SER	LYS	LYS	E	E	7 - 75	5 - 73
6	SER	SER	GLY	GLY	F	F	7 - 74	5 - 72
7	ASN	ASN	GLY	GLY	G	G	6 - 74	4 - 72
8	ASN	ASN	GLY	GLY	H	H	6 - 74	4 - 72
9	SER	SER	GLU	GLU	I	I	7 - 73	5 - 71
10	SER	SER	GLY	GLY	J	J	7 - 74	5 - 72
11	SER	SER	GLY	GLY	K	K	7 - 74	5 - 72
12	SER	SER	GLY	GLY	L	L	7 - 74	5 - 72
13	SER	SER	GLY	GLY	M	M	7 - 74	5 - 72
14	SER	SER	GLY	GLY	N	N	7 - 74	5 - 72
15	SER	SER	GLY	GLY	O	O	7 - 74	5 - 72
16	SER	SER	LYS	LYS	P	P	7 - 75	5 - 73
17	SER	SER	GLU	GLU	Q	Q	7 - 73	5 - 71
18	SER	SER	GLU	GLU	R	R	7 - 73	5 - 71
19	ASN	ASN	GLY	GLY	S	S	6 - 74	4 - 72
20	SER	SER	GLY	GLY	T	T	7 - 74	5 - 72
21	SER	SER	LYS	LYS	U	U	7 - 75	5 - 73
22	SER	SER	LYS	LYS	V	V	7 - 75	5 - 73

#1: Protein	... Transcription attenuation protein mtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein Mass: 8257.377 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: mtrB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X6J6
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

...
Transcription attenuation protein mtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein

Mass: 8257.377 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus stearothermophilus (bacteria) / Gene: mtrB / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9X6J6

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.03 Å³/Da / Density % sol: 39.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 400, 0.2M calcium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. all: 24780 / Num. obs: 23417 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / R_merge(I) obs: 0.082 / Net I/σ(I): 10.3

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAW

1qaw

Resolution: 3.2→20 Å / Cor.coef. F_o:F_c: 0.898 / Cor.coef. F_o:F_c free: 0.866 / SU B: 62.6 / SU ML: 0.484 / Cross valid method: THROUGHOUT / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2674	1174	5.1 %	RANDOM
R_work	0.2384	-	-	-
obs	0.2399	22011	95.94 %	-
all	-	22942	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 130.87 Å² / B_iso mean: 68.0068 Å² / B_iso min: 3.14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	-0 Å²	0.07 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	0.22 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10662	0	0	7	10669

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	10789
X-RAY DIFFRACTION	r_angle_refined_deg	1.321	1.931	14496
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.337	5	1351
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.856	24.318	491
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.803	15	1895
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.655	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1716
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7865
X-RAY DIFFRACTION	r_mcbond_it	1.649	1.5	6783
X-RAY DIFFRACTION	r_mcangle_it	3.097	2	10858
X-RAY DIFFRACTION	r_scbond_it	2.286	3	4006
X-RAY DIFFRACTION	r_scangle_it	4.022	4.5	3638

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	232	TIGHT POSITIONAL	0.04	0.05
2	B	232	TIGHT POSITIONAL	0.04	0.05
3	C	232	TIGHT POSITIONAL	0.05	0.05
4	D	232	TIGHT POSITIONAL	0.04	0.05
5	E	232	TIGHT POSITIONAL	0.04	0.05
6	F	232	TIGHT POSITIONAL	0.04	0.05
7	G	232	TIGHT POSITIONAL	0.03	0.05
8	H	232	TIGHT POSITIONAL	0.04	0.05
9	I	232	TIGHT POSITIONAL	0.03	0.05
10	J	232	TIGHT POSITIONAL	0.04	0.05
11	K	232	TIGHT POSITIONAL	0.03	0.05
12	L	232	TIGHT POSITIONAL	0.04	0.05
13	M	232	TIGHT POSITIONAL	0.04	0.05
14	N	232	TIGHT POSITIONAL	0.04	0.05
15	O	232	TIGHT POSITIONAL	0.03	0.05
16	P	232	TIGHT POSITIONAL	0.03	0.05
17	Q	232	TIGHT POSITIONAL	0.03	0.05
18	R	232	TIGHT POSITIONAL	0.03	0.05
19	S	232	TIGHT POSITIONAL	0.04	0.05
20	T	232	TIGHT POSITIONAL	0.04	0.05
21	U	232	TIGHT POSITIONAL	0.05	0.05
22	V	232	TIGHT POSITIONAL	0.04	0.05
1	A	182	MEDIUM POSITIONAL	0.05	0.5
2	B	182	MEDIUM POSITIONAL	0.04	0.5
3	C	182	MEDIUM POSITIONAL	0.04	0.5
4	D	182	MEDIUM POSITIONAL	0.04	0.5
5	E	182	MEDIUM POSITIONAL	0.04	0.5
6	F	182	MEDIUM POSITIONAL	0.04	0.5
7	G	182	MEDIUM POSITIONAL	0.04	0.5
8	H	182	MEDIUM POSITIONAL	0.05	0.5
9	I	182	MEDIUM POSITIONAL	0.03	0.5
10	J	182	MEDIUM POSITIONAL	0.04	0.5
11	K	182	MEDIUM POSITIONAL	0.04	0.5
12	L	182	MEDIUM POSITIONAL	0.04	0.5
13	M	182	MEDIUM POSITIONAL	0.04	0.5
14	N	182	MEDIUM POSITIONAL	0.05	0.5
15	O	182	MEDIUM POSITIONAL	0.04	0.5
16	P	182	MEDIUM POSITIONAL	0.04	0.5
17	Q	182	MEDIUM POSITIONAL	0.04	0.5
18	R	182	MEDIUM POSITIONAL	0.04	0.5
19	S	182	MEDIUM POSITIONAL	0.04	0.5
20	T	182	MEDIUM POSITIONAL	0.04	0.5
21	U	182	MEDIUM POSITIONAL	0.04	0.5
22	V	182	MEDIUM POSITIONAL	0.04	0.5
1	A	232	TIGHT THERMAL	0.07	0.5
2	B	232	TIGHT THERMAL	0.13	0.5
3	C	232	TIGHT THERMAL	0.16	0.5
4	D	232	TIGHT THERMAL	0.12	0.5
5	E	232	TIGHT THERMAL	0.06	0.5
6	F	232	TIGHT THERMAL	0.07	0.5
7	G	232	TIGHT THERMAL	0.08	0.5
8	H	232	TIGHT THERMAL	0.08	0.5
9	I	232	TIGHT THERMAL	0.08	0.5
10	J	232	TIGHT THERMAL	0.11	0.5
11	K	232	TIGHT THERMAL	0.09	0.5
12	L	232	TIGHT THERMAL	0.07	0.5
13	M	232	TIGHT THERMAL	0.07	0.5
14	N	232	TIGHT THERMAL	0.09	0.5
15	O	232	TIGHT THERMAL	0.09	0.5
16	P	232	TIGHT THERMAL	0.09	0.5
17	Q	232	TIGHT THERMAL	0.08	0.5
18	R	232	TIGHT THERMAL	0.09	0.5
19	S	232	TIGHT THERMAL	0.06	0.5
20	T	232	TIGHT THERMAL	0.1	0.5
21	U	232	TIGHT THERMAL	0.15	0.5
22	V	232	TIGHT THERMAL	0.14	0.5
1	A	182	MEDIUM THERMAL	0.07	2
2	B	182	MEDIUM THERMAL	0.13	2
3	C	182	MEDIUM THERMAL	0.15	2
4	D	182	MEDIUM THERMAL	0.12	2
5	E	182	MEDIUM THERMAL	0.06	2
6	F	182	MEDIUM THERMAL	0.07	2
7	G	182	MEDIUM THERMAL	0.07	2
8	H	182	MEDIUM THERMAL	0.07	2
9	I	182	MEDIUM THERMAL	0.09	2
10	J	182	MEDIUM THERMAL	0.1	2
11	K	182	MEDIUM THERMAL	0.08	2
12	L	182	MEDIUM THERMAL	0.07	2
13	M	182	MEDIUM THERMAL	0.07	2
14	N	182	MEDIUM THERMAL	0.09	2
15	O	182	MEDIUM THERMAL	0.09	2
16	P	182	MEDIUM THERMAL	0.08	2
17	Q	182	MEDIUM THERMAL	0.09	2
18	R	182	MEDIUM THERMAL	0.09	2
19	S	182	MEDIUM THERMAL	0.06	2
20	T	182	MEDIUM THERMAL	0.09	2
21	U	182	MEDIUM THERMAL	0.14	2
22	V	182	MEDIUM THERMAL	0.13	2

LS refinement shell

Resolution: 3.2→3.281 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	73	-
R_work	0.3	1410	-
all	-	1483	-
obs	-	-	85.08 %

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	0.2184	-0.1473	0.4427	0.7403	-0.0778	1.0564	0.0187	0.2461	0.074	-0.0781	-0.0597	-0.3214	0.0303	0.463	0.041	0.3107	0.0044	0.0477	0.362	0.0302	0.2863	0.06	4.703	-34.962
2	0.1889	-0.1649	0.3579	0.6153	-0.0521	1.0124	0.007	-0.067	-0.0289	0.0201	-0.0473	0.2842	-0.0502	-0.4252	0.0403	0.3262	0.029	0.0031	0.3598	-0.013	0.2925	-28.428	6.066	-27.9

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 75
2	X-RAY DIFFRACTION	1	B	7 - 75
3	X-RAY DIFFRACTION	1	C	7 - 74
4	X-RAY DIFFRACTION	1	D	7 - 74
5	X-RAY DIFFRACTION	1	E	7 - 75
6	X-RAY DIFFRACTION	1	F	7 - 74
7	X-RAY DIFFRACTION	1	G	6 - 74
8	X-RAY DIFFRACTION	1	H	6 - 74
9	X-RAY DIFFRACTION	1	I	7 - 73
10	X-RAY DIFFRACTION	1	J	7 - 74
11	X-RAY DIFFRACTION	1	K	7 - 74
12	X-RAY DIFFRACTION	2	L	7 - 74
13	X-RAY DIFFRACTION	2	M	7 - 74
14	X-RAY DIFFRACTION	2	N	7 - 74
15	X-RAY DIFFRACTION	2	O	7 - 74
16	X-RAY DIFFRACTION	2	P	7 - 75
17	X-RAY DIFFRACTION	2	Q	7 - 73
18	X-RAY DIFFRACTION	2	R	7 - 73
19	X-RAY DIFFRACTION	2	S	6 - 74
20	X-RAY DIFFRACTION	2	T	7 - 74
21	X-RAY DIFFRACTION	2	U	7 - 75
22	X-RAY DIFFRACTION	2	V	7 - 75

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