PDB-8h5s: Crystal structure of Rv3400 from Mycobacterium tuberculosis

ID or keywords:

Entry

Database: PDB / ID: 8h5s

Title

Crystal structure of Rv3400 from Mycobacterium tuberculosis

Components

Beta-phosphoglucomutase

Keywords

ISOMERASE / Beta-phosphoglucomutase / Haloacid dehalogenase family protein / crystal / G1P

Function / homology

Function and homology information

beta-phosphoglucomutase / isomerase activity / metal ion binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Singh, L. / Karthikeyan, S. / Thakur, K.G.

Funding support

India, 1items

Citation

Journal: Protein Sci. / Year: 2024
Title: Biochemical and structural characterization reveals Rv3400 codes for beta-phosphoglucomutase in Mycobacterium tuberculosis.
Authors: Singh, L. / Karthikeyan, S. / Thakur, K.G.

History

Deposition	Oct 13, 2022	Deposition site: PDBJ / Processing site: PDBE
Revision 1.0	Oct 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2	May 15, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8h5s.cif.gz	141.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8h5s.ent.gz	90.9 KB	Display	PDB format
PDBx/mmJSON format	8h5s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8h5s_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	8h5s_full_validation.pdf.gz	439.8 KB	Display
Data in XML	8h5s_validation.xml.gz	14.3 KB	Display
Data in CIF	8h5s_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5s ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5s	HTTPS FTP

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Related structure data

Similar structure data	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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (3) #118 - Oct 2009 Sodium-Potassium Pump similarity (1)

Deposited unit

A: Beta-phosphoglucomutase

hetero molecules

28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	97.903, 106.389, 81.204
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-304- CL
2	1	A-508- HOH
3	1	A-707- HOH

#1: Protein	Beta-phosphoglucomutase Mass: 28116.562 Da / Num. of mol.: 1 / Mutation: L126M, L197M, L202M, H123L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv3400, MTCY78.28c / Plasmid: pET DuetN-Rv3400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P9WKZ7
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.82 Å³/Da / Density % sol: 67.8 % / Description: Rectangular
Crystal grow	Temperature: 293 K / Method: microbatch / pH: 4.5 Details: 0.2 M Ammonium Sulphate 0.05 M sodium acetate pH 4.5 30% PEG 8000 PH range: 4-5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020
Radiation	Collimation: Mirrors were cylindrical collimating and Toroidal focussing mirror Monochromator: Double crystal monochromator / Analyzer: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.7→41.92 Å / Num. obs: 85784 / % possible obs: 95.4 % / Observed criterion σ(I): 1.6 / Redundancy: 11.1 % / B_iso Wilson estimate: 22.87 Å² / CC_1/2: 1 / R_merge(I) obs: 0.057 / Net I/σ(I): 30.3
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.676 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1601 / CC_1/2: 0.65 / % possible all: 66.2

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
PHENIX	1.20_4459	refinement
XDS	Jan 10, 2022	data reduction
XDS	Jan 10, 2022	data scaling
PHENIX	1.20-4459	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→33.34 Å / SU ML: 0.1645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1728	4163	4.85 %
R_work	0.154	81612	-
obs	0.1549	85775	94.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→33.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1852	0	12	310	2174

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1969
X-RAY DIFFRACTION	f_angle_d	0.7577	2680
X-RAY DIFFRACTION	f_chiral_restr	0.0528	303
X-RAY DIFFRACTION	f_plane_restr	0.0069	363
X-RAY DIFFRACTION	f_dihedral_angle_d	11.7814	725

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.72	0.3043	98	0.2869	1673	X-RAY DIFFRACTION	58.51
1.72-1.74	0.2669	108	0.2627	1970	X-RAY DIFFRACTION	69.38
1.74-1.76	0.3049	126	0.2464	2121	X-RAY DIFFRACTION	74.16
1.76-1.78	0.2054	124	0.2293	2359	X-RAY DIFFRACTION	82.03
1.78-1.81	0.2539	131	0.2522	2441	X-RAY DIFFRACTION	85.73
1.81-1.83	0.2276	126	0.2194	2550	X-RAY DIFFRACTION	90.47
1.83-1.86	0.2367	124	0.222	2746	X-RAY DIFFRACTION	94.38
1.86-1.88	0.173	130	0.2011	2785	X-RAY DIFFRACTION	97.59
1.88-1.91	0.2254	132	0.1921	2902	X-RAY DIFFRACTION	99.35
1.91-1.95	0.2227	136	0.1773	2832	X-RAY DIFFRACTION	99.7
1.95-1.98	0.184	185	0.1646	2859	X-RAY DIFFRACTION	100
1.98-2.01	0.1902	127	0.156	2875	X-RAY DIFFRACTION	100
2.01-2.05	0.2013	148	0.1556	2847	X-RAY DIFFRACTION	100
2.05-2.1	0.1397	147	0.1515	2841	X-RAY DIFFRACTION	100
2.1-2.14	0.1925	153	0.1618	2887	X-RAY DIFFRACTION	100
2.14-2.19	0.1838	122	0.146	2877	X-RAY DIFFRACTION	100
2.19-2.25	0.1511	118	0.1447	2856	X-RAY DIFFRACTION	100
2.25-2.31	0.1635	165	0.1399	2858	X-RAY DIFFRACTION	99.93
2.31-2.37	0.1566	176	0.153	2846	X-RAY DIFFRACTION	100
2.37-2.45	0.1813	164	0.1518	2828	X-RAY DIFFRACTION	99.97
2.45-2.54	0.1928	178	0.1704	2827	X-RAY DIFFRACTION	100
2.54-2.64	0.1883	153	0.1601	2852	X-RAY DIFFRACTION	99.93
2.64-2.76	0.1755	136	0.1744	2886	X-RAY DIFFRACTION	100
2.76-2.91	0.2092	117	0.1637	2895	X-RAY DIFFRACTION	100
2.91-3.09	0.1911	138	0.1614	2873	X-RAY DIFFRACTION	99.97
3.09-3.32	0.156	128	0.1508	2872	X-RAY DIFFRACTION	99.87
3.33-3.66	0.1757	166	0.1353	2844	X-RAY DIFFRACTION	100
3.66-4.19	0.1267	130	0.122	2888	X-RAY DIFFRACTION	99.97
4.19-5.27	0.1364	142	0.1211	2854	X-RAY DIFFRACTION	99.93
5.27-33.34	0.1403	135	0.1451	2868	X-RAY DIFFRACTION	99.17

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	2.71145703798	-2.57959975175	-1.15480512634	5.52040673803	0.799695663673	4.06094251282	-0.00938125324089	-0.0391700578015	0.261476732768	0.117619158601	0.0399293175797	0.175240455901	-0.129134964735	-0.266869589508	-0.0180811051218	0.155527056484	0.000258315584964	-0.000922882399853	0.167043927715	-0.00710817281406	0.14769948637	22.2362401134	39.6494788119	45.778097114
2	3.1583198644	-1.08389529055	-2.72264485272	0.759699101565	1.05461648653	5.51786337056	0.0188029373315	-0.0111702682266	0.0575142427412	-0.0147935362761	0.029848618697	-0.0334162683627	-0.057202027163	0.221475040317	-0.0587152369505	0.156334211373	-0.0232236726152	0.00268752390939	0.142783698949	0.00770017048967	0.194483092225	39.98122852	33.6057109762	23.7802408902
3	2.12322751326	1.05432865949	-0.324206388969	3.51537906268	-1.86871448782	3.08879774916	0.0767923268449	0.0658522827069	-0.0416013089244	-0.211618228843	-0.00892136367613	0.167726022006	0.261243753469	-0.00572879711999	-0.0755873413524	0.189822441181	0.00660838637456	-0.0189901355453	0.179303313415	-0.00892095230126	0.164685648906	33.3285765007	25.4307180975	20.5928142786
4	8.26903690493	0.577500459052	1.89308819907	6.16794883974	0.252017910069	4.47659554402	0.00786579743356	-0.498979268674	0.221521383995	0.707684385238	0.0866427315655	-0.590662106334	0.247840338274	0.270480101837	-0.0884760116473	0.251851331593	0.0510502366403	-0.0315853362994	0.175153103474	-0.0186598640365	0.230086193436	40.3201599159	24.2615930634	32.397699975
5	3.73831332963	-1.0494481844	-5.31072474429	4.51776329989	2.44475220559	8.60004503962	-0.230306660093	-0.555594377268	-0.133839298352	0.352116133941	0.306320094058	-0.405339154427	0.307244998917	0.690889259214	-0.0225161853375	0.211886538986	0.0356506193561	-0.0541208411381	0.197872358535	0.00355194619924	0.190836845743	30.96468353	38.6841892243	51.8778488066
6	2.73858646125	-0.701228661748	-2.72934492281	1.21742842482	1.71637823501	7.09956082868	-0.0945830957649	0.080633311411	-0.257436246348	0.159218076642	-0.0170213119091	-0.0589961300851	0.505911987319	0.184240341919	0.0895419095055	0.213390182717	-0.00293048792214	0.00239186370015	0.146042031427	0.0272557173905	0.218276363392	27.2752851539	29.1311983641	45.3965701453
7	2.33664251709	0.153310516894	1.52302645712	3.18813822097	-0.371575261341	6.5229108193	0.0573109282566	-0.0945489093598	-0.251384087688	0.0360659717756	-0.0212724622562	-0.0314030259685	0.840963627188	0.0197701664295	-0.0514934197053	0.211303815656	-0.0124764117032	0.0230575692921	0.163836122066	0.0204879957256	0.206659002364	22.6351932943	26.7037065655	40.5010333044
8	7.42806303907	-0.106741936877	-6.49635952233	2.88425371634	-0.861711203642	9.4074989211	-0.0959864982925	0.310034327354	-0.207755797768	-0.1316434711	0.126296865184	0.310834217364	0.525391793406	-0.948665840067	-0.0271737170059	0.177809317703	-0.0720628552351	-0.0131990671391	0.290576277956	0.0124364843359	0.266696014023	13.6592086578	30.7378063143	39.9027350268
9	3.0598841092	1.33591704624	0.508366554774	4.00919357327	0.0385962337755	3.23910242629	-0.0224330036867	0.0723986528472	0.0200536746756	-0.147224595712	0.05865901953	-0.0305985790257	-0.184448680769	-0.123436072903	-0.0404924597927	0.134394732231	0.0263020803811	0.00746887581161	0.108025066519	-0.00244483073531	0.143399083388	23.9970862299	45.1303827747	37.7267635605

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 16 through 37 )	16 - 37	1 - 22
2	2	chain 'A' and (resid 38 through 81 )	38 - 81	23 - 66
3	3	chain 'A' and (resid 82 through 110 )	82 - 110	67 - 95
4	4	chain 'A' and (resid 111 through 128 )	111 - 128	96 - 113
5	5	chain 'A' and (resid 129 through 146 )	129 - 146	114 - 131
6	6	chain 'A' and (resid 147 through 167 )	147 - 167	132 - 152
7	7	chain 'A' and (resid 168 through 193 )	168 - 193	153 - 178
8	8	chain 'A' and (resid 194 through 206 )	194 - 206	179 - 191
9	9	chain 'A' and (resid 207 through 262 )	207 - 262	192 - 247

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