PDB-4zgl: Hit Like Protein

ID or keywords:

Entry

Database: PDB / ID: 4zgl

Title

Hit Like Protein

Components

Uncharacterized HIT-like protein HP_0404

Keywords

CELL CYCLE

Function / homology

Function and homology information

D-alanine catabolic process / adenosine 5'-monophosphoramidase activity / cytoplasm / cytosol
Similarity search - Function

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of HINT from Helicobacter pylori.
Authors: Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S.

History

Deposition	Apr 23, 2015	Deposition site: RCSB / Processing site: PDBJ
Supersession	May 27, 2015	ID: 4Q61
Revision 1.0	May 27, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 13, 2016	Group: Database references
Revision 1.2	Oct 4, 2017	Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Jan 1, 2020	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4	Nov 8, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zgl.cif.gz	404 KB	Display	PDBx/mmCIF format
PDB format	pdb4zgl.ent.gz	334 KB	Display	PDB format
PDBx/mmJSON format	4zgl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zgl_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	4zgl_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4zgl_validation.xml.gz	35.2 KB	Display
Data in CIF	4zgl_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zg/4zgl ftp://data.pdbj.org/pub/pdb/validation_reports/zg/4zgl	HTTPS FTP

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Related structure data

Related structure data	1xqu PDB Unreleased entryS S: Starting model for refinement
Similar structure data	6we4-1 7l9y-3 7l9y-2 7lun-7 3eja-2 3k24-1 6fvj-7 7lun-8 4e88-d 3eop-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1xqu
PDB Unreleased entryS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (3) #86 - Feb 2007 Exosomes similarity (3) #245 - May 2020 Spliceosomes similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#145 - Jan 2012
Messenger RNA Capping
similarity (3)
#86 - Feb 2007
Exosomes
similarity (3)
#245 - May 2020
Spliceosomes
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#24 - Dec 2001
Glycogen Phosphorylase
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)

Deposited unit

A: Uncharacterized HIT-like protein HP_0404

B: Uncharacterized HIT-like protein HP_0404

C: Uncharacterized HIT-like protein HP_0404

D: Uncharacterized HIT-like protein HP_0404

E: Uncharacterized HIT-like protein HP_0404

F: Uncharacterized HIT-like protein HP_0404

G: Uncharacterized HIT-like protein HP_0404

H: Uncharacterized HIT-like protein HP_0404

I: Uncharacterized HIT-like protein HP_0404

J: Uncharacterized HIT-like protein HP_0404

hetero molecules

131 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized HIT-like protein HP_0404

B: Uncharacterized HIT-like protein HP_0404

hetero molecules

defined by author&software
26.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uncharacterized HIT-like protein HP_0404

D: Uncharacterized HIT-like protein HP_0404

hetero molecules

defined by author&software
26.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Uncharacterized HIT-like protein HP_0404

F: Uncharacterized HIT-like protein HP_0404

hetero molecules

defined by author&software
26.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Uncharacterized HIT-like protein HP_0404

H: Uncharacterized HIT-like protein HP_0404

hetero molecules

defined by author&software
26.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Uncharacterized HIT-like protein HP_0404

J: Uncharacterized HIT-like protein HP_0404

hetero molecules

defined by author&software
26.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.900, 75.640, 335.090
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	1 - 100
2	1	B	1 - 100
1	2	A	1 - 101
2	2	C	1 - 101
1	3	A	1 - 100
2	3	D	1 - 100
1	4	A	1 - 100
2	4	F	1 - 100
1	5	A	1 - 101
2	5	G	1 - 101
1	6	A	1 - 101
2	6	H	1 - 101
1	7	A	1 - 100
2	7	I	1 - 100
1	8	A	1 - 101
2	8	J	1 - 101
1	9	B	1 - 100
2	9	C	1 - 100
1	10	B	1 - 102
2	10	D	1 - 102
1	11	B	1 - 102
2	11	F	1 - 102
1	12	B	1 - 100
2	12	G	1 - 100
1	13	B	1 - 100
2	13	H	1 - 100
1	14	B	1 - 102
2	14	I	1 - 102
1	15	B	1 - 100
2	15	J	1 - 100
1	16	C	1 - 100
2	16	D	1 - 100
1	17	C	1 - 100
2	17	F	1 - 100
1	18	C	1 - 101
2	18	G	1 - 101
1	19	C	1 - 101
2	19	H	1 - 101
1	20	C	1 - 100
2	20	I	1 - 100
1	21	C	1 - 101
2	21	J	1 - 101
1	22	D	1 - 102
2	22	F	1 - 102
1	23	D	1 - 100
2	23	G	1 - 100
1	24	D	1 - 100
2	24	H	1 - 100
1	25	D	1 - 102
2	25	I	1 - 102
1	26	D	1 - 100
2	26	J	1 - 100
1	27	F	1 - 100
2	27	G	1 - 100
1	28	F	1 - 100
2	28	H	1 - 100
1	29	F	1 - 102
2	29	I	1 - 102
1	30	F	1 - 100
2	30	J	1 - 100
1	31	G	1 - 101
2	31	H	1 - 101
1	32	G	1 - 100
2	32	I	1 - 100
1	33	G	1 - 101
2	33	J	1 - 101
1	34	H	1 - 100
2	34	I	1 - 100
1	35	H	1 - 101
2	35	J	1 - 101
1	36	I	1 - 100
2	36	J	1 - 100

NCS ensembles :

#1: Protein	Uncharacterized HIT-like protein HP_0404 Mass: 12943.020 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: HP_0404 / Production host: Escherichia coli (E. coli) / References: UniProt: P64382
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% PEG 3350, 12.5% PEG 1000, 12.5% MPD, 0.03M AMINO ACID

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 30, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 2.95→41.07 Å / Num. obs: 25808 / % possible obs: 96.1 % / Redundancy: 6.1 % / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.95→3.1 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.826 / Mean I/σ(I) obs: 2.2 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1XQU

1xqu
PDB Unreleased entry

Resolution: 2.95→41.07 Å / Cor.coef. F_o:F_c: 0.878 / Cor.coef. F_o:F_c free: 0.863 / SU B: 52.23 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R: 4.234 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28153	1298	5 %	RANDOM
R_work	0.26474	-	-	-
obs	0.26559	24499	94.5 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 57.444 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.97 Å²	0 Å²	-0 Å²
2-	-	2.05 Å²	-0 Å²
3-	-	-	-1.08 Å²

Refinement step

Cycle: 1 / Resolution: 2.95→41.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7933	0	115	0	8048

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	8235
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	8158
X-RAY DIFFRACTION	r_angle_refined_deg	1.485	1.982	11084
X-RAY DIFFRACTION	r_angle_other_deg	1.663	3	18856
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.121	5	986
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.512	25.877	359
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.473	15	1571
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.914	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.151	0.2	1242
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	9035
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1814
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_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	6091	0.11
1	2	B	6091	0.11
2	1	A	6043	0.11
2	2	C	6043	0.11
3	1	A	5890	0.11
3	2	D	5890	0.11
4	1	A	6009	0.11
4	2	F	6009	0.11
5	1	A	5950	0.13
5	2	G	5950	0.13
6	1	A	6014	0.12
6	2	H	6014	0.12
7	1	A	6053	0.11
7	2	I	6053	0.11
8	1	A	6161	0.11
8	2	J	6161	0.11
9	1	B	5961	0.12
9	2	C	5961	0.12
10	1	B	5937	0.12
10	2	D	5937	0.12
11	1	B	6110	0.11
11	2	F	6110	0.11
12	1	B	6001	0.12
12	2	G	6001	0.12
13	1	B	5939	0.12
13	2	H	5939	0.12
14	1	B	6122	0.1
14	2	I	6122	0.1
15	1	B	6087	0.11
15	2	J	6087	0.11
16	1	C	5782	0.12
16	2	D	5782	0.12
17	1	C	5918	0.12
17	2	F	5918	0.12
18	1	C	5969	0.11
18	2	G	5969	0.11
19	1	C	5975	0.11
19	2	H	5975	0.11
20	1	C	5974	0.11
20	2	I	5974	0.11
21	1	C	6095	0.1
21	2	J	6095	0.1
22	1	D	6205	0.1
22	2	F	6205	0.1
23	1	D	6019	0.11
23	2	G	6019	0.11
24	1	D	6013	0.12
24	2	H	6013	0.12
25	1	D	6092	0.1
25	2	I	6092	0.1
26	1	D	5888	0.12
26	2	J	5888	0.12
27	1	F	5987	0.12
27	2	G	5987	0.12
28	1	F	6116	0.12
28	2	H	6116	0.12
29	1	F	6129	0.1
29	2	I	6129	0.1
30	1	F	6034	0.11
30	2	J	6034	0.11
31	1	G	5921	0.13
31	2	H	5921	0.13
32	1	G	6286	0.09
32	2	I	6286	0.09
33	1	G	6122	0.11
33	2	J	6122	0.11
34	1	H	5932	0.12
34	2	I	5932	0.12
35	1	H	6032	0.12
35	2	J	6032	0.12
36	1	I	6127	0.11
36	2	J	6127	0.11

LS refinement shell

Resolution: 2.95→3.027 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.385	93	-
R_work	0.364	1819	-
obs	-	-	95.89 %

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	3.7764	-0.9432	0.4282	1.896	-0.5384	3.7751	-0.1651	-0.0476	0.0332	-0.0911	0.1814	0.3252	-0.1441	-0.708	-0.0163	0.3993	-0.0244	0.029	0.3995	0.0533	0.1188	-23.838	0.221	-78.201
2	3.6077	0.4731	-0.4863	2.4413	-0.4311	6.1487	-0.1744	0.1898	0.1557	0.0637	0.0432	-0.2799	-0.1821	0.4259	0.1311	0.322	-0.0214	0.0047	0.2305	-0.0322	0.1178	-3.406	0.794	-73.841
3	2.7077	1.0981	-1.0449	4.3509	0.0744	4.1798	-0.0214	0.1471	0.0251	0.0059	0.0442	-0.0024	0.2057	-0.1943	-0.0229	0.4018	0.0206	-0.0366	0.0405	0.0357	0.056	-0.359	-41.36	-23.855
4	3.8559	0.2893	-0.4683	1.8646	-0.199	4.9237	0.1019	-0.034	0.3068	0.0714	-0.0608	-0.2583	-0.3233	0.8243	-0.0411	0.5239	-0.1121	-0.0253	0.1577	0.0208	0.0917	17.51	-29.802	-25.372
5	1.6781	-0.9075	2.1546	3.1453	0.464	6.3257	0.0657	-0.2185	0.2332	-0.3196	-0.3777	0.1062	-0.9326	-1.0079	0.3121	0.7655	0.3066	0.0279	0.3778	-0.0125	0.1151	-19.293	12.147	-39.576
6	1.8322	-0.1871	0.0166	3.4904	1.0277	5.399	-0.0453	0.0916	-0.0398	0.2645	-0.0305	0.0132	0.1563	-0.3964	0.0758	0.3828	0.0213	0.0235	0.0616	-0.0071	0.0032	-11.485	-7.351	-43.823
7	2.88	0.4591	-0.8017	3.6755	0.6281	5.0245	-0.0339	-0.1477	0.3408	0.0523	-0.0054	0.1225	-0.4352	-0.3944	0.0394	0.4526	0.0711	-0.036	0.1211	-0.0471	0.1291	-1.07	-31.738	7.67
8	3.2711	-0.4351	1.4035	3.7917	0.6337	4.9206	-0.0189	-0.0189	-0.0718	-0.0559	-0.0393	-0.0666	-0.1732	0.089	0.0582	0.3512	0.017	-0.0063	0.0112	-0.0053	0.0182	13.881	-46.504	10.342
9	2.7167	-0.4651	0.0846	2.5299	0.692	4.3294	0.0966	-0.3029	-0.3195	-0.0678	-0.0409	0.0841	0.6882	-0.2977	-0.0557	0.6187	-0.1539	-0.0233	0.1397	0.0379	0.1286	-15.204	-7.924	-108.413
10	3.2665	0.2965	0.4668	3.3611	-0.9382	4.6021	0.1159	-0.0147	0.1114	-0.0398	-0.1488	-0.1243	-0.1862	0.0901	0.0329	0.4079	-0.0617	0.0395	0.0391	-0.0183	0.0423	-9.231	12.171	-110.595

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 101
2	X-RAY DIFFRACTION	2	B	1 - 101
3	X-RAY DIFFRACTION	3	C	1 - 101
4	X-RAY DIFFRACTION	4	D	1 - 102
5	X-RAY DIFFRACTION	5	E	3 - 102
6	X-RAY DIFFRACTION	6	F	1 - 102
7	X-RAY DIFFRACTION	7	G	1 - 101
8	X-RAY DIFFRACTION	8	H	1 - 101
9	X-RAY DIFFRACTION	9	I	1 - 102
10	X-RAY DIFFRACTION	10	J	1 - 101

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-Yorodumi

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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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

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Yorodumi