PDB-7oy9: Crystal structure of GMP reductase from mycobacterium smegmatis.

ID or keywords:

Entry

Database: PDB / ID: 7oy9

Title

Crystal structure of GMP reductase from mycobacterium smegmatis.

Components

Guanosine 5'-monophosphate reductase

Keywords

OXIDOREDUCTASE / GMP reductase GMPR oxidoreductase GuaB1 octamer CBS domain Bateman domain Mycobacterium smegmatis

Function / homology

:

Function and homology information

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Dolezal, M. / Klima, M. / Pichova, I.

Funding support

Czech Republic, 1items

Citation

Journal: Febs J. / Year: 2022
Title: The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-beta-synthase domain.
Authors: Knejzlik, Z. / Dolezal, M. / Herkommerova, K. / Clarova, K. / Klima, M. / Dedola, M. / Zbornikova, E. / Rejman, D. / Pichova, I.

History

Deposition	Jun 24, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 27, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7oy9.cif.gz	782.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7oy9.ent.gz	523.5 KB	Display	PDB format
PDBx/mmJSON format	7oy9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7oy9_validation.pdf.gz	507.4 KB	Display	wwPDB validaton report
Full document	7oy9_full_validation.pdf.gz	545.8 KB	Display
Data in XML	7oy9_validation.xml.gz	114.6 KB	Display
Data in CIF	7oy9_validation.cif.gz	156.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/7oy9 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oy9	HTTPS FTP

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Related structure data

Related structure data	7r50C 1zfjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Guanosine 5'-monophosphate reductase

B: Guanosine 5'-monophosphate reductase

C: Guanosine 5'-monophosphate reductase

D: Guanosine 5'-monophosphate reductase

E: Guanosine 5'-monophosphate reductase

F: Guanosine 5'-monophosphate reductase

G: Guanosine 5'-monophosphate reductase

H: Guanosine 5'-monophosphate reductase

414 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Guanosine 5'-monophosphate reductase

B: Guanosine 5'-monophosphate reductase

C: Guanosine 5'-monophosphate reductase

D: Guanosine 5'-monophosphate reductase

defined by author&software
Evidence: gel filtration
207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Guanosine 5'-monophosphate reductase

F: Guanosine 5'-monophosphate reductase

G: Guanosine 5'-monophosphate reductase

H: Guanosine 5'-monophosphate reductase

defined by author&software
Evidence: gel filtration
207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	253.06, 109.83, 200.82
Angle α, β, γ (deg.)	90.0, 119.429, 90.0
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLY	GLY	chain 'A'	A	A	1 - 386	1 - 386
1	2	ASP	ASP	GLU	GLU	chain 'A'	A	A	400 - 412	400 - 412
1	3	ARG	ARG	PHE	PHE	chain 'A'	A	A	419 - 469	419 - 469
2	4	MET	MET	GLY	GLY	chain 'B'	B	B	1 - 386	1 - 386
2	5	ASP	ASP	GLU	GLU	chain 'B'	B	B	400 - 412	400 - 412
2	6	ARG	ARG	PHE	PHE	chain 'B'	B	B	419 - 469	419 - 469
3	7	MET	MET	GLY	GLY	chain 'C'	C	C	1 - 386	1 - 386
3	8	ASP	ASP	GLU	GLU	chain 'C'	C	C	400 - 412	400 - 412
3	9	ARG	ARG	PHE	PHE	chain 'C'	C	C	419 - 469	419 - 469
4	10	MET	MET	GLY	GLY	chain 'D'	D	D	1 - 386	1 - 386
4	11	ASP	ASP	GLU	GLU	chain 'D'	D	D	400 - 412	400 - 412
4	12	ARG	ARG	PHE	PHE	chain 'D'	D	D	419 - 469	419 - 469
5	13	MET	MET	GLY	GLY	chain 'E'	E	E	1 - 386	1 - 386
5	14	ASP	ASP	GLU	GLU	chain 'E'	E	E	400 - 412	400 - 412
5	15	ARG	ARG	PHE	PHE	chain 'E'	E	E	419 - 469	419 - 469
6	16	MET	MET	GLY	GLY	chain 'F'	F	F	1 - 386	1 - 386
6	17	ASP	ASP	GLU	GLU	chain 'F'	F	F	400 - 412	400 - 412
6	18	ARG	ARG	PHE	PHE	chain 'F'	F	F	419 - 469	419 - 469
7	19	MET	MET	GLY	GLY	chain 'G'	G	G	1 - 386	1 - 386
7	20	ASP	ASP	GLU	GLU	chain 'G'	G	G	400 - 412	400 - 412
7	21	ARG	ARG	PHE	PHE	chain 'G'	G	G	419 - 469	419 - 469
8	22	MET	MET	GLY	GLY	chain 'H'	H	H	1 - 386	1 - 386
8	23	ASP	ASP	GLU	GLU	chain 'H'	H	H	400 - 412	400 - 412
8	24	ARG	ARG	PHE	PHE	chain 'H'	H	H	419 - 469	419 - 469

#1: Protein	Guanosine 5'-monophosphate reductase / Guanosine 5'-monophosphate reductase Mass: 51782.434 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Guanosine 5'-monophosphate reductase / Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: guaB_2, ERS451418_03599 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6IET0, GMP reductase

#1: Protein

Guanosine 5'-monophosphate reductase / Guanosine 5'-monophosphate reductase

Mass: 51782.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Guanosine 5'-monophosphate reductase / Source: (gene. exp.)

Mycolicibacterium smegmatis (bacteria) / Gene: guaB_2, ERS451418_03599 / Plasmid: pTriex / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6IET0, GMP reductase

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.93	58.07
2
3

Crystal grow

Temperature (K)	Crystal-ID	Method	Details
291	1	vapor diffusion, hanging drop	0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 10.0% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.5
291	2	vapor diffusion, hanging drop	0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 10.0% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.5
291	3	vapor diffusion, hanging drop	0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 11.5% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.8→43.73 Å / Num. obs: 118145 / % possible obs: 99.89 % / Redundancy: 39.7 % / B_iso Wilson estimate: 94.66 Å² / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.1555 / R_pim(I) all: 0.02519 / R_rim(I) all: 0.1575 / Net I/σ(I): 17.77
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 40.9 % / R_merge(I) obs: 3.968 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 11722 / CC_1/2: 0.662 / CC star: 0.892 / R_pim(I) all: 0.6261 / R_rim(I) all: 4.018 / % possible all: 99.94

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Coot	0.9	model building
XDS	February 5, 2021	data reduction
XSCALE	February 5, 2021	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1zfj

1zfj

Resolution: 2.8→43.7268094132 Å / SU ML: 0.505527372014 / Cross valid method: FREE R-VALUE / σ(F): 1.33786841327 / Phase error: 36.2922566505

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274950470775	5903	5.00004235171 %	random selection
R_work	0.234286072604	112156	-	-
obs	0.236369725587	118059	99.9212878326 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 114.339674134 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→43.7268094132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25837	0	0	0	25837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00991484754362	26263
X-RAY DIFFRACTION	f_angle_d	1.22104371939	35895
X-RAY DIFFRACTION	f_chiral_restr	0.0539937513943	4380
X-RAY DIFFRACTION	f_plane_restr	0.00964722368175	4738
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3840003748	8962

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 (%)
2.8-2.8318	0.442668444525	196	0.410030982195	3723	X-RAY DIFFRACTION	99.9489926039
2.8318-2.8651	0.4577474313	197	0.383084303344	3750	X-RAY DIFFRACTION	99.9746707194
2.8651-2.9001	0.411105218795	193	0.395066842587	3659	X-RAY DIFFRACTION	99.8962655602
2.9001-2.9368	0.43299801193	198	0.376466772452	3754	X-RAY DIFFRACTION	99.9494183106
2.9368-2.9754	0.426855862233	195	0.345521513753	3700	X-RAY DIFFRACTION	99.9743326489
2.9754-3.0161	0.429921408693	195	0.365422786286	3716	X-RAY DIFFRACTION	99.9744376278
3.0161-3.0592	0.411093000902	197	0.361632855322	3742	X-RAY DIFFRACTION	100
3.0592-3.1049	0.402933305713	196	0.324197276026	3712	X-RAY DIFFRACTION	99.9744180097
3.1049-3.1534	0.344725050219	195	0.30972119167	3708	X-RAY DIFFRACTION	99.9231950845
3.1534-3.2051	0.376355497284	197	0.301511234581	3740	X-RAY DIFFRACTION	99.9492256918
3.2051-3.2603	0.327343677017	196	0.308386300881	3735	X-RAY DIFFRACTION	99.9491482329
3.2603-3.3196	0.37873736131	195	0.29661027003	3696	X-RAY DIFFRACTION	99.9743062693
3.3196-3.3834	0.368447804189	196	0.300479795772	3732	X-RAY DIFFRACTION	99.9745482311
3.3834-3.4524	0.338681916274	197	0.293705309783	3745	X-RAY DIFFRACTION	99.8986315256
3.4524-3.5275	0.369604147436	197	0.299706234605	3739	X-RAY DIFFRACTION	100
3.5275-3.6095	0.344672872681	194	0.292768591906	3690	X-RAY DIFFRACTION	100
3.6095-3.6997	0.284474832733	197	0.282431554667	3730	X-RAY DIFFRACTION	100
3.6997-3.7997	0.351803993358	197	0.262263838759	3736	X-RAY DIFFRACTION	99.9745805796
3.7997-3.9114	0.276599314271	197	0.251308973978	3745	X-RAY DIFFRACTION	100
3.9114-4.0376	0.269452513691	198	0.237610686609	3765	X-RAY DIFFRACTION	100
4.0376-4.1818	0.273408450678	196	0.237220293124	3724	X-RAY DIFFRACTION	100
4.1818-4.3491	0.256945745464	196	0.230625570775	3716	X-RAY DIFFRACTION	99.9233716475
4.3491-4.5468	0.236173942887	197	0.217362177963	3750	X-RAY DIFFRACTION	99.9746707194
4.5468-4.7863	0.25046664448	199	0.20057504142	3783	X-RAY DIFFRACTION	99.9247176913
4.7863-5.0857	0.247138463625	197	0.208357213341	3737	X-RAY DIFFRACTION	100
5.0857-5.4777	0.267107899559	198	0.220466445343	3769	X-RAY DIFFRACTION	100
5.4777-6.0277	0.23463392449	198	0.216610550279	3755	X-RAY DIFFRACTION	100
6.0277-6.897	0.244537366861	199	0.194890749875	3786	X-RAY DIFFRACTION	99.9498369702
6.897-8.6783	0.207291511546	200	0.174362991949	3789	X-RAY DIFFRACTION	100
8.6783-43.7268094132	0.220399127685	200	0.184442329191	3830	X-RAY DIFFRACTION	98.5812133072

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