PDB-6v77: Crystal structure of a putative HpcE protein from Mycobacterium s...

ID or keywords:

Entry

Database: PDB / ID: 6v77

Title

Crystal structure of a putative HpcE protein from Mycobacterium smegmatis

Components

Putative HpcE protein

Keywords

UNKNOWN FUNCTION / SSGCID / HpcE protein / Mycobacerium smegmatis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

catalytic activity / metal ion binding
Similarity search - Function

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of a putative HpcE protein from Mycobacterium smegmatis
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 7, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6v77.cif.gz	237.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6v77.ent.gz	189.7 KB	Display	PDB format
PDBx/mmJSON format	6v77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6v77_validation.pdf.gz	275.6 KB	Display	wwPDB validaton report
Full document	6v77_full_validation.pdf.gz	275.6 KB	Display
Data in XML	6v77_validation.xml.gz	1.4 KB	Display
Data in CIF	6v77_validation.cif.gz	9.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/6v77 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v77	HTTPS FTP

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Related structure data

Related structure data	1i7oS 3lrkS S: Starting model for refinement
Similar structure data	2q3d-1 6a37-d 3gwd-d 4tya-3 4ore-1 3vc3-3 4u65-1 2qe2-1 4wtc-d 6mvq-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MysmA.00471.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative HpcE protein

B: Putative HpcE protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	68.250, 68.250, 218.980
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-210- ARG
2	1	B-591- HOH

#1: Protein	Putative HpcE protein Mass: 31739.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2007 / Plasmid: MysmA.00471.a.AE1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0QTY3
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47.1 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 22 mg/mL MysmA.00471.a.AE1.PW38681 against Microlytic/Anatrace MCSG-1 screen condition H7 (2000 mM ammonium sulfate, 100 mM Bis-Tris/HCl, pH 5.5), cryoprotectant: 25% ethylene glycol in 2 ...Details: 22 mg/mL MysmA.00471.a.AE1.PW38681 against Microlytic/Anatrace MCSG-1 screen condition H7 (2000 mM ammonium sulfate, 100 mM Bis-Tris/HCl, pH 5.5), cryoprotectant: 25% ethylene glycol in 2 steps, tray 311974h7, puck uac1-9

Crystal

Density Matthews: 2.32 Å³/Da / Density % sol: 47.1 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22 mg/mL MysmA.00471.a.AE1.PW38681 against Microlytic/Anatrace MCSG-1 screen condition H7 (2000 mM ammonium sulfate, 100 mM Bis-Tris/HCl, pH 5.5), cryoprotectant: 25% ethylene glycol in 2 ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 25, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.75→45.93 Å / Num. obs: 60836 / % possible obs: 100 % / Redundancy: 7.276 % / B_iso Wilson estimate: 31.31 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_rim(I) all: 0.057 / Χ²: 1.027 / Net I/σ(I): 20.89 / Num. measured all: 442650 / Scaling rejects: 11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.75-1.8	7.36	0.492	3.96	32590	4428	4428	0.931	0.53	100
1.8-1.84	7.38	0.39	4.85	31897	4322	4322	0.961	0.42	100
1.84-1.9	7.394	0.298	6.37	30899	4179	4179	0.973	0.32	100
1.9-1.96	7.379	0.219	8.48	30159	4088	4087	0.989	0.236	100
1.96-2.02	7.403	0.187	9.76	29169	3941	3940	0.988	0.201	100
2.02-2.09	7.381	0.149	12.16	28108	3808	3808	0.992	0.16	100
2.09-2.17	7.379	0.114	15.22	27642	3746	3746	0.995	0.123	100
2.17-2.26	7.366	0.098	17.7	26341	3576	3576	0.996	0.106	100
2.26-2.36	7.348	0.083	20.44	25453	3464	3464	0.997	0.089	100
2.36-2.47	7.339	0.074	22.8	23968	3266	3266	0.997	0.08	100
2.47-2.61	7.323	0.063	25.93	23163	3164	3163	0.998	0.068	100
2.61-2.77	7.284	0.057	28.53	21517	2954	2954	0.998	0.061	100
2.77-2.96	7.214	0.047	33.02	20611	2857	2857	0.999	0.051	100
2.96-3.2	7.214	0.043	37.8	18714	2595	2594	0.999	0.046	100
3.2-3.5	7.095	0.038	41.24	17242	2432	2430	0.999	0.041	99.9
3.5-3.91	7.055	0.036	43.77	15577	2208	2208	0.999	0.039	100
3.91-4.52	7.038	0.034	46	13963	1984	1984	0.999	0.037	100
4.52-5.53	6.92	0.033	46.18	11625	1680	1680	0.999	0.036	100
5.53-7.83	6.834	0.034	45.44	9281	1358	1358	0.999	0.036	100
7.83-45.93	5.973	0.037	43.84	4731	812	792	0.998	0.041	97.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.17.1	refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1I7O & 3LRK

1i7o

3lrk

Resolution: 1.75→45.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.11

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2002	2083	3.43 %	0
R_work	0.1598	-	-	-
obs	0.1611	60744	99.94 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 113.44 Å² / B_iso mean: 31.9973 Å² / B_iso min: 12.58 Å²

Refinement step

Cycle: final / Resolution: 1.75→45.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4146	0	57	481	4684
B_iso mean	-	-	70.07	39.59	-
Num. residues	-	-	-	-	550

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4376
X-RAY DIFFRACTION	f_angle_d	0.907	5996
X-RAY DIFFRACTION	f_dihedral_angle_d	18.46	1575
X-RAY DIFFRACTION	f_chiral_restr	0.064	668
X-RAY DIFFRACTION	f_plane_restr	0.006	801

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.75-1.79	0.2261	152	0.1999	3819	3971
1.79-1.84	0.2436	143	0.2043	3813	3956
1.84-1.89	0.2291	123	0.1935	3865	3988
1.89-1.94	0.2222	159	0.1839	3856	4015
1.94-2	0.2443	137	0.1783	3848	3985
2-2.07	0.1998	146	0.1753	3863	4009
2.07-2.16	0.1899	135	0.1599	3842	3977
2.16-2.26	0.2155	150	0.1568	3881	4031
2.26-2.38	0.2245	142	0.1573	3890	4032
2.38-2.52	0.2158	122	0.1601	3927	4049
2.52-2.72	0.2399	134	0.1681	3915	4049
2.72-2.99	0.2197	142	0.1684	3927	4069
2.99-3.42	0.1806	130	0.1593	3977	4107
3.43-4.31	0.1743	119	0.1391	4034	4153
4.32-45.93	0.1758	149	0.151	4204	4353

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	3.3859	-1.1878	-0.1736	5.3087	-0.1708	6.4458	-0.1608	-0.0294	0.1925	0.2817	-0.0432	0.2661	-0.3194	-0.3572	0.2233	0.2213	-0.0586	-0.025	0.2685	-0.0423	0.2056	-30.4024	15.9041	-3.6665
2	-0.0092	-0.0515	0.2351	2.1528	1.8587	3.8936	-0.0647	0.0301	0.0568	-0.0341	-0.0207	0.0864	-0.3179	-0.3002	0.0792	0.1669	-0.0705	0.0028	0.282	-0.0149	0.2299	-30.1279	13.3563	-11.0694
3	1.7879	0.3301	-0.3887	1.538	-0.2569	2.1792	-0.1273	0.2199	-0.1969	-0.131	0.126	-0.2931	0.125	0.4892	0.0577	0.1479	-0.1077	0.0136	0.4194	-0.0561	0.2535	-20.5059	-3.5999	-21.904
4	1.1563	0.1119	0.1115	1.6052	-0.2623	1.0002	-0.0461	0.0902	-0.0875	-0.0453	0.0639	-0.139	-0.0131	0.079	-0.0283	0.134	-0.0977	0.0052	0.3184	-0.0161	0.2089	-21.5063	0.0006	-18.1911
5	1.8698	0.2224	0.8679	0.8292	-0.3146	1.8855	-0.0012	0.1904	-0.2126	-0.0991	0.023	-0.1858	0.0852	0.3076	0.0055	0.1828	-0.1111	0.0149	0.3441	-0.0394	0.2693	-16.5045	0.9566	-20.9766
6	1.1105	1.6019	0.8011	8.9498	0.2228	2.2476	0.1101	-0.1243	-0.2981	0.4899	-0.0835	-0.4889	0.2387	0.3575	-0.0454	0.1428	-0.0765	-0.057	0.4085	0.0276	0.3047	-14.5749	-7.448	-6.6333
7	2.4355	-2.1623	-1.4853	4.7945	-0.7975	2.5102	-0.1103	0.1306	0.2287	0.0875	0.0408	0.052	-0.2713	0.078	0.0662	0.1879	-0.1198	-0.0358	0.3394	-0.014	0.2393	-57.4011	2.572	-21.1434
8	2.9103	-0.1481	-0.49	0.8478	0.6048	1.214	-0.0693	-0.0217	0.0201	-0.044	0.1122	0.283	-0.1484	-0.212	-0.0396	0.1665	-0.0899	-0.0251	0.4159	0.0138	0.3034	-63.0626	-1.161	-19.5315
9	0.9592	0.1364	0.0832	0.7717	-0.2891	0.9689	-0.087	0.2175	-0.0472	-0.1605	0.1043	-0.0388	0.1231	-0.0065	-0.0071	0.2088	-0.137	0.015	0.354	-0.0199	0.2154	-39.2307	-9.5004	-30.4229
10	3.4563	-0.8149	1.7467	2.166	1.2272	2.2317	-0.0361	-0.1277	-0.3143	0.2558	0.2506	0.2642	0.2518	-0.3357	-0.1907	0.1613	-0.143	-0.0022	0.2986	-0.0105	0.2139	-48.773	-15.1903	-21.2583
11	0.6465	0.2295	0.2481	1.032	-0.0996	1.101	-0.0762	0.2101	-0.0713	-0.169	0.113	-0.0759	0.0997	0.0883	-0.0348	0.2093	-0.135	0.0082	0.3693	-0.0287	0.2181	-41.4276	-12.9062	-32.0061
12	1.9276	-0.5859	-0.8872	1.0712	0.2464	1.5106	0.0796	0.431	0.0639	-0.212	-0.0112	-0.0986	0.0182	-0.0289	-0.0789	0.2692	-0.1527	-0.0148	0.4834	0.0202	0.2301	-43.377	-7.3567	-45.4351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )	A	1 - 32
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 76 )	A	33 - 76
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 109 )	A	77 - 109
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 195 )	A	110 - 195
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 196 through 248 )	A	196 - 248
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 249 through 277 )	A	249 - 277
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 39 )	B	1 - 39
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 59 )	B	40 - 59
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 60 through 136 )	B	60 - 136
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 137 through 151 )	B	137 - 151
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 152 through 248 )	B	152 - 248
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 249 through 279 )	B	249 - 279

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