PDB-4h4l: Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)

Basic information

• Entry: Database: PDB / ID: 4h4l
• Title: Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)
• Components: Hut operon positive regulatory protein
• Keywords: RNA BINDING PROTEIN / HUTP / ANTI-TERMINATION / HISTIDINE METABOLISM / TRANSCRIPTION / TRANSCRIPTION REGULATION

Function / homology

Function:

L-histidine metabolic process / mRNA binding / positive regulation of gene expression

Domain/homology:

Hut operon positive regulatory protein HutP / Hut operon regulatory protein HutP / Hut operon regulatory protein HutP / Hut operon regulatory protein HutP, bacillales / Hut operon regulatory protein HutP superfamily / HutP / 3-Layer(aba) Sandwich / Alpha Beta

Component:

HISTIDINE / Hut operon positive regulatory protein

• Biological species: Bacillus subtilis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
• Authors: Dhakshnamoorthy, B. / Misono, T.S. / Mizuno, H. / Kumar, P.K.R.
• Citation: Journal: J.Struct.Biol. / Year: 2013; Title: Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis.; Authors: Dhakshnamoorthy, B. / Mizuno, H. / Kumar, P.K.R.

History

Deposition	Sep 17, 2012	Deposition site: RCSB / Processing site: PDBJ
Supersession	Sep 4, 2013	ID: 2ZH0
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Nov 8, 2023	Group: Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Hut operon positive regulatory protein

B: Hut operon positive regulatory protein

C: Hut operon positive regulatory protein

D: Hut operon positive regulatory protein

E: Hut operon positive regulatory protein

F: Hut operon positive regulatory protein

G: Hut operon positive regulatory protein

H: Hut operon positive regulatory protein

I: Hut operon positive regulatory protein

J: Hut operon positive regulatory protein

K: Hut operon positive regulatory protein

L: Hut operon positive regulatory protein

hetero molecules

Summary:

• 197 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	197,449	36
Polymers	194,791	12
Non-polymers	2,659	24
Water	1,459	81

1

A: Hut operon positive regulatory protein

B: Hut operon positive regulatory protein

C: Hut operon positive regulatory protein

J: Hut operon positive regulatory protein

K: Hut operon positive regulatory protein

L: Hut operon positive regulatory protein

hetero molecules

Summary:

• defined by author&software
• 98.7 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,725	18
Polymers	97,395	6
Non-polymers	1,329	12
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	19270 Å2
ΔGint	-320 kcal/mol
Surface area	28570 Å2
Method	PISA

2

D: Hut operon positive regulatory protein

E: Hut operon positive regulatory protein

F: Hut operon positive regulatory protein

G: Hut operon positive regulatory protein

H: Hut operon positive regulatory protein

I: Hut operon positive regulatory protein

hetero molecules

Summary:

• defined by author&software
• 98.7 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,725	18
Polymers	97,395	6
Non-polymers	1,329	12
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	19130 Å2
ΔGint	-320 kcal/mol
Surface area	28770 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	129.530, 129.530, 76.670
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Components on special symmetry positions

ID	Model	Components
1	1	C-310- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 2 - 148 / Label seq-ID: 2 - 148

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A B C D E F G H I J K L
Hut operon positive regulatory protein

Details:

Mass: 16232.553 Da / Num. of mol.: 12 / Mutation: V51I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU39340, hutP / Plasmid: PET5A / Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P10943

#2: Chemical

A-201 B-201 C-201 D-201 D-203 F-201 G-201 G-203 I-201 J-201 J-203 L-201
ChemComp-HIS / HISTIDINE / Histidine

Details:

Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₆H₁₀N₃O₂

#3: Chemical

A-202 B-202 C-202 D-202 E-201 F-202 G-202 H-201 I-202 J-202 K-201 L-202
ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 1.91 ų/Da / Density % sol: 35.48 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 ; Details: 30% PEG 2K MME, 0.1M HEPES PH7.6, 0.5M KBR, 10MM ZINC ACETATE, 0.2M L-HIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.25363 Å
• Detector: Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.25363 Å / Relative weight: 1
• Reflection: Resolution: 2.3→50 Å / Num. all: 57983 / Num. obs: 57983 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / R_merge(I) obs: 0.119 / Net I/σ(I): 15.7
• Reflection shell: Resolution: 2.3→2.38 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.515 / Mean I/σ(I) obs: 1.1 / % possible all: 52

Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VEA

1vea

Resolution: 2.5→36.28 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.908 / SU B: 15.332 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.29778	2508	5.1 %	RANDOM
Rwork	0.21931	-	-	-
obs	0.22331	46338	98.12 %	-
all	-	49771	-	-

• 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: 57.165 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.02 Å2	-0.01 Å2	0 Å2
2-	-	-0.02 Å2	0 Å2
3-	-	-	0.03 Å2

Refinement step

Cycle: LAST / Resolution: 2.5→36.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12822	0	144	81	13047

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	13160
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.626	1.96	17718
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.643	5	1682
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.781	22.789	527
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.102	15	2171
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.588	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	2054
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9716
X-RAY DIFFRACTION	r_gen_planes_other
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	161	0.09
1	2	B	161	0.09
2	1	A	161	0.1
2	2	C	161	0.1
3	1	A	179	0.01
3	2	D	179	0.01
4	1	A	160	0.12
4	2	E	160	0.12
5	1	A	163	0.1
5	2	F	163	0.1
6	1	A	167	0.11
6	2	G	167	0.11
7	1	A	154	0.16
7	2	H	154	0.16
8	1	A	160	0.13
8	2	I	160	0.13
9	1	A	170	0.11
9	2	J	170	0.11
10	1	A	153	0.13
10	2	K	153	0.13
11	1	A	162	0.12
11	2	L	162	0.12
12	1	B	157	0.13
12	2	C	157	0.13
13	1	B	160	0.09
13	2	D	160	0.09
14	1	B	181	0.01
14	2	E	181	0.01
15	1	B	163	0.13
15	2	F	163	0.13
16	1	B	159	0.16
16	2	G	159	0.16
17	1	B	173	0.09
17	2	H	173	0.09
18	1	B	157	0.15
18	2	I	157	0.15
19	1	B	161	0.16
19	2	J	161	0.16
20	1	B	171	0.08
20	2	K	171	0.08
21	1	B	156	0.14
21	2	L	156	0.14
22	1	C	161	0.1
22	2	D	161	0.1
23	1	C	155	0.1
23	2	E	155	0.1
24	1	C	179	0.01
24	2	F	179	0.01
25	1	C	160	0.1
25	2	G	160	0.1
26	1	C	151	0.13
26	2	H	151	0.13
27	1	C	173	0.08
27	2	I	173	0.08
28	1	C	163	0.12
28	2	J	163	0.12
29	1	C	151	0.12
29	2	K	151	0.12
30	1	C	175	0.08
30	2	L	175	0.08
31	1	D	161	0.12
31	2	E	161	0.12
32	1	D	166	0.1
32	2	F	166	0.1
33	1	D	169	0.11
33	2	G	169	0.11
34	1	D	157	0.15
34	2	H	157	0.15
35	1	D	162	0.13
35	2	I	162	0.13
36	1	D	172	0.11
36	2	J	172	0.11
37	1	D	152	0.14
37	2	K	152	0.14
38	1	D	163	0.12
38	2	L	163	0.12
39	1	E	161	0.13
39	2	F	161	0.13
40	1	E	160	0.16
40	2	G	160	0.16
41	1	E	174	0.11
41	2	H	174	0.11
42	1	E	158	0.11
42	2	I	158	0.11
43	1	E	162	0.16
43	2	J	162	0.16
44	1	E	169	0.08
44	2	K	169	0.08
45	1	E	156	0.1
45	2	L	156	0.1
46	1	F	166	0.12
46	2	G	166	0.12
47	1	F	159	0.15
47	2	H	159	0.15
48	1	F	174	0.09
48	2	I	174	0.09
49	1	F	169	0.13
49	2	J	169	0.13
50	1	F	155	0.14
50	2	K	155	0.14
51	1	F	173	0.08
51	2	L	173	0.08
52	1	G	161	0.16
52	2	H	161	0.16
53	1	G	162	0.14
53	2	I	162	0.14
54	1	G	184	0.01
54	2	J	184	0.01
55	1	G	154	0.14
55	2	K	154	0.14
56	1	G	161	0.13
56	2	L	161	0.13
57	1	H	157	0.1
57	2	I	157	0.1
58	1	H	162	0.16
58	2	J	162	0.16
59	1	H	175	0.01
59	2	K	175	0.01
60	1	H	156	0.09
60	2	L	156	0.09
61	1	I	167	0.15
61	2	J	167	0.15
62	1	I	156	0.11
62	2	K	156	0.11
63	1	I	179	0.05
63	2	L	179	0.05
64	1	J	156	0.14
64	2	K	156	0.14
65	1	J	167	0.14
65	2	L	167	0.14
66	1	K	155	0.1
66	2	L	155	0.1

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.388	158	-
Rwork	0.305	3000	-
obs	-	-	86.17 %