PDB-4r7k: 1.88 Angstrom Resolution Crystal Structure of Hypothetical Protei...

ID or keywords:

Entry

Database: PDB / ID: 4r7k

Title

1.88 Angstrom Resolution Crystal Structure of Hypothetical Protein jhp0584 from Helicobacter pylori.

Components

Hypothetical protein jhp0584

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Putative

Function and homology information

Biological species

Helicobacter pylori J99 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.88 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 1.88 Angstrom Resolution Crystal Structure of Hypothetical Protein jhp0584 from Helicobacter pylori.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 27, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Nov 6, 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 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r7k.cif.gz	300.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4r7k.ent.gz	246.4 KB	Display	PDB format
PDBx/mmJSON format	4r7k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4r7k_validation.pdf.gz	452.5 KB	Display	wwPDB validaton report
Full document	4r7k_full_validation.pdf.gz	455.2 KB	Display
Data in XML	4r7k_validation.xml.gz	35.3 KB	Display
Data in CIF	4r7k_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/4r7k ftp://data.pdbj.org/pub/pdb/validation_reports/r7/4r7k	HTTPS FTP

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Related structure data

Similar structure data	1e4e-d 6hyt-1 6hys-2 6ye0-d 6hys-1 2jim-d 4wtk-d 1e5v-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-idp06192

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein jhp0584

B: Hypothetical protein jhp0584

C: Hypothetical protein jhp0584

D: Hypothetical protein jhp0584

90.2 kDa, 4 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)	67.832, 70.945, 86.454
Angle α, β, γ (deg.)	90.00, 91.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypothetical protein jhp0584 Mass: 22554.604 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori J99 (bacteria) / Strain: J99 / Gene: jhp0584, jhp_0584 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9ZLJ5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.63 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Protein: 7.7 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME; Screen: PACT (G11), 0.1M MMT buffer (pH 9.0), 25%(w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97892 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2014 / Details: Beryllium lenese
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97892 Å / Relative weight: 1
Reflection	Resolution: 1.88→30 Å / Num. all: 66450 / Num. obs: 66450 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 27.9 Å² / R_merge(I) obs: 0.081 / R_sym value: 0.081 / Net I/σ(I): 24.3
Reflection shell	Resolution: 1.88→1.91 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.534 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3305 / R_sym value: 0.534 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.7.0032	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.88→27.43 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.664 / SU ML: 0.086
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20746	3360	5.1 %	RANDOM
R_work	0.17084	-	-	-
all	0.17268	63040	-	-
obs	0.17268	63040	99.35 %	-

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: 34.992 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	-0.11 Å²
2-	-	-0.8 Å²	0 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→27.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5544	0	0	448	5992

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	5812
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5436
X-RAY DIFFRACTION	r_angle_refined_deg	1.495	1.936	7890
X-RAY DIFFRACTION	r_angle_other_deg	0.708	3	12483
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.53	5	696
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.288	24.419	301
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.133	15	942
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.483	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	822
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6669
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1439
X-RAY DIFFRACTION	r_mcbond_it	1.637	1.938	2754
X-RAY DIFFRACTION	r_mcbond_other	1.638	1.937	2753
X-RAY DIFFRACTION	r_mcangle_it	2.361	2.894	3460
X-RAY DIFFRACTION	r_mcangle_other	2.361	2.895	3461
X-RAY DIFFRACTION	r_scbond_it	2.666	2.245	3058
X-RAY DIFFRACTION	r_scbond_other	2.662	2.245	3058
X-RAY DIFFRACTION	r_scangle_other	3.977	3.236	4430
X-RAY DIFFRACTION	r_long_range_B_refined	6.215	16.923	6833
X-RAY DIFFRACTION	r_long_range_B_other	6.125	16.389	6640

LS refinement shell

Resolution: 1.88→1.929 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	240	-
R_work	0.225	4481	-
obs	-	4481	96.43 %

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	1.0871	-0.2904	0.1123	1.2285	-0.0532	1.2285	0.0069	0.0935	-0.1451	-0.029	-0.0099	0.0609	0.039	-0.0223	0.0029	0.0296	-0.0287	-0.0066	0.0663	-0.0248	0.065	17.6719	9.5004	21.1047
2	3.125	0.8821	0.1737	3.6669	-1.3824	2.9113	0.0032	0.1682	-0.6023	-0.1161	-0.1328	-0.125	0.4825	0.1251	0.1296	0.1637	0.0302	0.0173	0.0371	-0.0726	0.2335	27.4627	-5.8966	19.0568
3	9.4763	-2.7238	4.3133	3.315	-2.4226	6.9271	-0.0461	-0.14	-0.6014	0.0052	0.1186	0.0734	0.3293	-0.1094	-0.0724	0.172	-0.0292	0.0376	0.0334	-0.0599	0.2117	19.944	-2.3901	22.9448
4	1.6696	0.395	0.1154	1.0887	0.312	1.8167	-0.0067	-0.0026	-0.2732	0.0373	-0.0053	-0.0896	0.1764	0.0405	0.012	0.049	-0.0125	-0.0038	0.0193	-0.0133	0.0987	22.728	5.4772	25.5109
5	1.5178	0.8123	1.0283	1.8698	1.4281	3.3513	-0.0404	0.1135	-0.1685	-0.1124	-0.0219	-0.1502	0.0011	0.1539	0.0624	0.0479	0.0023	-0.0044	0.0843	-0.042	0.0967	30.7173	10.6395	19.0262
6	0.7052	0.3029	-0.307	1.2506	-0.6159	1.4054	0.054	-0.1092	-0.0343	0.2245	-0.1159	-0.0358	-0.1695	0.1159	0.0619	0.0748	-0.0064	-0.0392	0.1309	0.0637	0.0855	55.7615	12.9341	35.7411
7	8.5829	-7.8854	1.9367	14.6357	-3.9854	1.0965	0.3174	0.0997	-0.4604	-0.3284	-0.0836	0.9029	0.086	0.032	-0.2337	0.0869	0.0141	-0.0402	0.1413	0.0533	0.1409	43.6346	5.1241	37.6925
8	4.6287	3.1103	0.6407	5.0601	-0.9045	2.3738	0.0134	-0.1092	-0.2656	0.0719	-0.146	-0.2788	0.141	0.1253	0.1327	0.0377	0.0042	-0.0046	0.1255	0.0787	0.0692	58.2294	6.7558	36.5569
9	2.1105	1.1723	0.6901	3.4765	0.3163	1.9526	0.0348	-0.0304	0.0211	0.1131	-0.1065	0.0712	-0.0325	-0.0136	0.0718	0.0114	0.017	-0.0007	0.1221	0.054	0.0685	53.8266	10.7215	27.6619
10	2.0361	0.7617	1.0038	2.9814	1.7683	4.8759	-0.0009	-0.0445	0.0726	0.1389	0.0216	0.0251	-0.3233	-0.1507	-0.0207	0.0751	0.0177	0.0058	0.0899	0.0443	0.0528	47.5832	18.7948	30.0578
11	2.3106	-1.8036	0.5593	2.1859	-0.5275	2.1069	-0.0587	0.2046	0.1862	0.1281	-0.0174	-0.1125	-0.3225	0.2031	0.0761	0.0794	-0.0495	-0.0196	0.1267	0.0816	0.1239	61.9817	25.9092	19.001
12	1.1188	-0.061	0.1413	2.6354	-1.6332	1.564	0.0504	0.2304	-0.0306	-0.4507	-0.0486	0.0585	0.2731	0.015	-0.0017	0.1311	0.0123	-0.0073	0.1698	0.0656	0.0583	53.9096	17.9472	1.196
13	16.9187	9.1226	-6.9779	16.0538	-7.642	4.2302	0.3202	-0.2305	0.2237	0.3406	0.0811	1.0131	-0.1914	0.0333	-0.4013	0.1147	-0.0046	-0.0024	0.2249	0.113	0.1533	44.7975	28.3485	4.7051
14	1.4771	-0.3621	-0.2434	2.3178	-0.8662	2.2146	-0.0107	0.1451	0.126	-0.0699	-0.0737	-0.0782	-0.166	0.0558	0.0844	0.0352	-0.007	-0.0178	0.1394	0.0805	0.0778	56.8032	23.9989	10.6719
15	2.8915	-0.104	-1.6682	3.3313	1.7578	5.2113	-0.0623	0.1108	-0.0843	-0.1268	-0.0177	0.2212	0.1514	-0.1174	0.08	0.0446	-0.0013	-0.0284	0.1419	0.0594	0.0596	47.2488	16.189	13.7676
16	0.8008	-0.0174	0.0018	1.5806	0.3469	1.1904	0.048	-0.023	0.1255	-0.1072	0.0044	-0.0015	-0.1131	-0.0368	-0.0524	0.0451	0.0226	0.0048	0.0651	-0.0204	0.0639	17.1285	23.99	22.6309
17	0.9372	-0.0178	-0.322	8.2449	-3.8117	3.1693	-0.1412	-0.2598	0.6696	0.11	0.161	-0.8406	-0.7361	0.4309	-0.0198	0.4904	-0.137	0.0404	0.2769	-0.1953	0.6381	26.8858	39.7095	27.7622
18	14.6113	-2.981	-2.7089	4.6165	-1.8947	3.9116	0.3819	0.108	0.1049	0.0774	-0.3295	-0.2136	-0.4541	0.4343	-0.0524	0.2761	-0.0497	0.012	0.076	-0.0642	0.2599	25.3811	39.4966	19.9846
19	1.7716	-0.4532	-0.6139	1.5041	0.1471	2.6148	0.0432	0.0236	0.293	-0.183	-0.0275	-0.171	-0.4424	-0.0141	-0.0157	0.1156	0.0025	0.0203	0.0115	-0.0108	0.0953	21.2217	30.1207	19.1131
20	2.5571	-1.3361	-1.3028	1.7539	1.6575	3.4956	0.0436	-0.2165	0.3187	0.0834	0.0587	-0.1433	-0.1406	0.1602	-0.1023	0.0477	-0.0277	0.0216	0.0857	-0.0541	0.1144	30.0891	23.508	25.419

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 40
2	X-RAY DIFFRACTION	2	A	41 - 78
3	X-RAY DIFFRACTION	3	A	79 - 92
4	X-RAY DIFFRACTION	4	A	93 - 144
5	X-RAY DIFFRACTION	5	A	145 - 167
6	X-RAY DIFFRACTION	6	B	0 - 73
7	X-RAY DIFFRACTION	7	B	74 - 83
8	X-RAY DIFFRACTION	8	B	84 - 108
9	X-RAY DIFFRACTION	9	B	109 - 147
10	X-RAY DIFFRACTION	10	B	148 - 167
11	X-RAY DIFFRACTION	11	C	0 - 23
12	X-RAY DIFFRACTION	12	C	24 - 73
13	X-RAY DIFFRACTION	13	C	74 - 83
14	X-RAY DIFFRACTION	14	C	84 - 144
15	X-RAY DIFFRACTION	15	C	145 - 167
16	X-RAY DIFFRACTION	16	D	0 - 39
17	X-RAY DIFFRACTION	17	D	40 - 65
18	X-RAY DIFFRACTION	18	D	66 - 79
19	X-RAY DIFFRACTION	19	D	80 - 144
20	X-RAY DIFFRACTION	20	D	145 - 167

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