PDB-7o0a: Bdellovibrio bacteriovorus PGI in P1211 spacegroup

ID or keywords:

Entry

Database: PDB / ID: 7o0a

Title

Bdellovibrio bacteriovorus PGI in P1211 spacegroup

Components

Glucose-6-phosphate isomerase

Keywords

ISOMERASE / PGI / phosphoglucose isomerase / GPI / glucose-6-phosphate isomerase

Function / homology

Function and homology information

glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function

Biological species

Bdellovibrio bacteriovorus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Meek, R.W. / Lovering, A.L.

Funding support

United Kingdom, 1items

Citation

Journal: Open Biology / Year: 2021
Title: Bdellovibrio bacteriovorus phosphoglucose isomerase structures reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding.
Authors: Meek, R.W. / Cadby, I.T. / Lovering, A.L.

History

Deposition	Mar 26, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 18, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 6, 2021	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _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	7o0a.cif.gz	707.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7o0a_validation.pdf.gz	441.7 KB	Display	wwPDB validaton report
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Related structure data

Related structure data	7nssSC 7ntgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7nss-1 7ntg-1 7o0a-4 7o0a-2 7o0a-3 1zzg-d 2xe4-d 7c66-d 5bpf-1 3ifs-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7nssSC

7ntgC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (8) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (8)

Deposited unit

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

C: Glucose-6-phosphate isomerase

D: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

G: Glucose-6-phosphate isomerase

H: Glucose-6-phosphate isomerase

E: Glucose-6-phosphate isomerase

hetero molecules

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

1

A: Glucose-6-phosphate isomerase

E: Glucose-6-phosphate isomerase

hetero molecules

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

2

B: Glucose-6-phosphate isomerase

G: Glucose-6-phosphate isomerase

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

3

C: Glucose-6-phosphate isomerase

H: Glucose-6-phosphate isomerase

hetero molecules

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

4

D: Glucose-6-phosphate isomerase

F: Glucose-6-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.920, 118.100, 138.980
Angle α, β, γ (deg.)	90.000, 118.410, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	A	A	3 - 405	3 - 405
2	1	LEU	LEU	B	B	3 - 405	3 - 405
1	2	LYS	LYS	A	A	3 - 406	3 - 406
2	2	LYS	LYS	C	C	3 - 406	3 - 406
1	3	LEU	LEU	A	A	3 - 405	3 - 405
2	3	LEU	LEU	D	D	3 - 405	3 - 405
1	4	LEU	LEU	A	A	3 - 405	3 - 405
2	4	LEU	LEU	F	E	3 - 405	3 - 405
1	5	LYS	LYS	A	A	3 - 406	3 - 406
2	5	LYS	LYS	G	F	3 - 406	3 - 406
1	6	LYS	LYS	A	A	3 - 406	3 - 406
2	6	LYS	LYS	H	G	3 - 406	3 - 406
1	7	LEU	LEU	A	A	3 - 405	3 - 405
2	7	LEU	LEU	E	H	3 - 405	3 - 405
1	8	LEU	LEU	B	B	3 - 405	3 - 405
2	8	LEU	LEU	C	C	3 - 405	3 - 405
1	9	LYS	LYS	B	B	3 - 407	3 - 407
2	9	LYS	LYS	D	D	3 - 407	3 - 407
1	10	LYS	LYS	B	B	3 - 407	3 - 407
2	10	LYS	LYS	F	E	3 - 407	3 - 407
1	11	LEU	LEU	B	B	3 - 405	3 - 405
2	11	LEU	LEU	G	F	3 - 405	3 - 405
1	12	LEU	LEU	B	B	3 - 405	3 - 405
2	12	LEU	LEU	H	G	3 - 405	3 - 405
1	13	LYS	LYS	B	B	3 - 407	3 - 407
2	13	LYS	LYS	E	H	3 - 407	3 - 407
1	14	LEU	LEU	C	C	3 - 405	3 - 405
2	14	LEU	LEU	D	D	3 - 405	3 - 405
1	15	LEU	LEU	C	C	3 - 405	3 - 405
2	15	LEU	LEU	F	E	3 - 405	3 - 405
1	16	LYS	LYS	C	C	3 - 406	3 - 406
2	16	LYS	LYS	G	F	3 - 406	3 - 406
1	17	LYS	LYS	C	C	3 - 406	3 - 406
2	17	LYS	LYS	H	G	3 - 406	3 - 406
1	18	LEU	LEU	C	C	3 - 405	3 - 405
2	18	LEU	LEU	E	H	3 - 405	3 - 405
1	19	LYS	LYS	D	D	3 - 407	3 - 407
2	19	LYS	LYS	F	E	3 - 407	3 - 407
1	20	LEU	LEU	D	D	3 - 405	3 - 405
2	20	LEU	LEU	G	F	3 - 405	3 - 405
1	21	LEU	LEU	D	D	3 - 405	3 - 405
2	21	LEU	LEU	H	G	3 - 405	3 - 405
1	22	LYS	LYS	D	D	3 - 407	3 - 407
2	22	LYS	LYS	E	H	3 - 407	3 - 407
1	23	LEU	LEU	F	E	3 - 405	3 - 405
2	23	LEU	LEU	G	F	3 - 405	3 - 405
1	24	LEU	LEU	F	E	3 - 405	3 - 405
2	24	LEU	LEU	H	G	3 - 405	3 - 405
1	25	LYS	LYS	F	E	3 - 407	3 - 407
2	25	LYS	LYS	E	H	3 - 407	3 - 407
1	26	LYS	LYS	G	F	3 - 406	3 - 406
2	26	LYS	LYS	H	G	3 - 406	3 - 406
1	27	LEU	LEU	G	F	3 - 405	3 - 405
2	27	LEU	LEU	E	H	3 - 405	3 - 405
1	28	LEU	LEU	H	G	3 - 405	3 - 405
2	28	LEU	LEU	E	H	3 - 405	3 - 405

NCS ensembles :

#1: Protein	Glucose-6-phosphate isomerase Mass: 48055.336 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria) Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: pgi, Bd0741 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MPU9, glucose-6-phosphate isomerase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3254 / 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: 2.59 Å³/Da / Density % sol: 52.5 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.2 M ammonium acetate 0.1 M sodium acetate pH4.0 15% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.74→59.54 Å / Num. obs: 395364 / % possible obs: 98.8 % / Redundancy: 3.9 % / CC_1/2: 0.982 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.073 / R_rim(I) all: 0.116 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.74→1.77 Å / R_merge(I) obs: 0.607 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 29299 / CC_1/2: 0.615 / R_pim(I) all: 0.495 / R_rim(I) all: 0.788

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7NSS

7nss

Resolution: 1.74→59.54 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2528	20056	5.1 %	RANDOM
R_work	0.2223	-	-	-
obs	0.2238	375276	98.74 %	-

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 max: 72.85 Å² / B_iso mean: 21.168 Å² / B_iso min: 4.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.37 Å²	0 Å²	0.05 Å²
2-	-	-1.37 Å²	-0 Å²
3-	-	-	0.6 Å²

Refinement step

Cycle: final / Resolution: 1.74→59.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25476	0	24	3254	28754
B_iso mean	-	-	30.73	30.93	-
Num. residues	-	-	-	-	3236

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	26617
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	25984
X-RAY DIFFRACTION	r_angle_refined_deg	1.341	1.633	35974
X-RAY DIFFRACTION	r_angle_other_deg	2.243	1.578	60027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.214	5	3380
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.796	22.947	1276
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.402	15	5063
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.101	15	145
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	3409
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	29940
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	5938

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	13626	0.06
1	2	B	13626	0.06
2	1	A	13685	0.05
2	2	C	13685	0.05
3	1	A	13588	0.06
3	2	D	13588	0.06
4	1	A	13567	0.06
4	2	F	13567	0.06
5	1	A	13610	0.06
5	2	G	13610	0.06
6	1	A	13623	0.06
6	2	H	13623	0.06
7	1	A	13527	0.06
7	2	E	13527	0.06
8	1	B	13866	0.05
8	2	C	13866	0.05
9	1	B	13869	0.06
9	2	D	13869	0.06
10	1	B	13879	0.06
10	2	F	13879	0.06
11	1	B	13834	0.05
11	2	G	13834	0.05
12	1	B	13829	0.06
12	2	H	13829	0.06
13	1	B	13855	0.06
13	2	E	13855	0.06
14	1	C	13787	0.05
14	2	D	13787	0.05
15	1	C	13728	0.06
15	2	F	13728	0.06
16	1	C	13739	0.06
16	2	G	13739	0.06
17	1	C	13733	0.06
17	2	H	13733	0.06
18	1	C	13691	0.06
18	2	E	13691	0.06
19	1	D	13860	0.06
19	2	F	13860	0.06
20	1	D	13785	0.05
20	2	G	13785	0.05
21	1	D	13789	0.05
21	2	H	13789	0.05
22	1	D	13816	0.05
22	2	E	13816	0.05
23	1	F	13616	0.05
23	2	G	13616	0.05
24	1	F	13633	0.06
24	2	H	13633	0.06
25	1	F	13682	0.05
25	2	E	13682	0.05
26	1	G	13803	0.05
26	2	H	13803	0.05
27	1	G	13768	0.05
27	2	E	13768	0.05
28	1	H	13728	0.06
28	2	E	13728	0.06

LS refinement shell

Resolution: 1.74→1.785 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	1463	-
R_work	0.295	27786	-
all	-	29249	-
obs	-	-	98.96 %

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