PDB-2r4j: Crystal structure of Escherichia coli SeMet substituted Glycerol-...

ID or keywords:

Entry

Database: PDB / ID: 2r4j

Title

Crystal structure of Escherichia coli SeMet substituted Glycerol-3-phosphate Dehydrogenase in complex with DHAP

Components

Aerobic glycerol-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / GlpD / FAD /

Flavoprotein / Glycerol metabolism

Function / homology

Function and homology information

glycerol-3-phosphate dehydrogenase /

glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / glycerol catabolic process / FAD binding /

electron transfer activity / protein homodimerization activity /

plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.96 Å

Authors

Yeh, J.I. / Du, S. / Chinte, U.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Authors: Yeh, J.I. / Chinte, U. / Du, S.

History

Deposition	Aug 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 3, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r4/2r4j ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r4j	HTTPS FTP

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Related structure data

Related structure data	2qcuC 2r45C 2r46C 2r4eC C: citing same article (ref.)
Similar structure data	2r46-1 4g01-d 5o9x-d 5osi-3 1ije-d 1dpp-2 1z6a-d 1w9m-d 5osi-4 6yju-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) 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	#50 - Feb 2004 Glycolytic Enzymes similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Aerobic glycerol-3-phosphate dehydrogenase

B: Aerobic glycerol-3-phosphate dehydrogenase

hetero molecules

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

1

A: Aerobic glycerol-3-phosphate dehydrogenase

hetero molecules

defined by author&software
60.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Aerobic glycerol-3-phosphate dehydrogenase

hetero molecules

defined by author&software
60.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	113.916, 114.142, 193.591
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 5 - 494 / Label seq-ID: 5 - 494

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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Protein / Sugars , 2 types, 8 molecules AB

#1: Protein

Aerobic glycerol-3-phosphate dehydrogenase

Mass: 57157.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: glpD, glyD / Production host:

Escherichia coli (E. coli) / References: UniProt: P13035, EC: 1.1.99.5

#2: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside /

Octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 8 types, 319 molecules

#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#5: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₅N₂
#7: Chemical	ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#8: Chemical	ChemComp-BCN / BICINE / Bicine Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: pH buffer*YM
#9: Chemical	ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₇NO₃ / Comment: pH buffer*YM
#10: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.31 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M di-Ammonium hydrogen phosphate, 0.1M Bicine, 12% w/v PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97928, 0.97947, 0.97181

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97928	1
2	0.97947	1
3	0.97181	1

Reflection

Redundancy: 6.3 % / Av σ(I) over netI: 13.2 / Number: 551112 / R_merge(I) obs: 0.113 / Χ²: 1.33 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 87054 / % possible obs: 96.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.2	50	97.8	1	0.082	0.971	6.9
3.33	4.2	99.9	1	0.096	0.957	7.3
2.91	3.33	100	1	0.119	1.18	7.1
2.65	2.91	100	1	0.163	1.279	7.1
2.46	2.65	99.9	1	0.232	1.388	7.1
2.31	2.46	99.8	1	0.322	1.475	7
2.2	2.31	99.6	1	0.423	1.656	6.3
2.1	2.2	98.1	1	0.467	1.6	5.4
2.02	2.1	89.3	1	0.549	1.652	4.6
1.95	2.02	80.6	1	0.614	1.63	3.8

Reflection

Resolution: 1.96→50 Å / Num. obs: 87054 / % possible obs: 96.5 % / Redundancy: 6.3 % / R_merge(I) obs: 0.113 / Net I/σ(I): 13.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	% possible all
1.96-2.02	3.8	0.614	80.6
2.02-2.1	4.6	0.549	89.3
2.1-2.2	5.4	0.467	98.1
2.2-2.31	6.3	0.423	99.6
2.31-2.46	7	0.322	99.8
2.46-2.65	7.1	0.232	99.9
2.65-2.91	7.1	0.163	100
2.91-3.33	7.1	0.119	100
3.33-4.2	7.3	0.096	99.9
4.2-50	6.9	0.082	97.8

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 2.02 Å / D res low: 50 Å / FOM : 0.31 / Reflection: 79066

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9793	2.67	-8.23
1	3 wavelength	2	0.9718	2.25	-3.4
1	3 wavelength	3	0.9795	2.66	-10.28

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	33.921	0.845	0.217	0.113	0.839
2	Se	20.547	0.865	0.246	0.145	0.737
3	Se	26.158	0.253	0.364	0.145	0.931
4	Se	60	0.769	0.137	0.128	1.401
5	Se	60	0.079	0.094	0.142	1.271
6	Se	40.586	0.362	0.269	0.128	0.806
7	Se	52.257	0.676	0.284	0.04	1.153
8	Se	24.638	0.281	0.345	0.114	0.653
9	Se	60	0.594	0.422	0.142	1.414
10	Se	60	0.663	0.219	0.069	1.005
11	Se	33.545	0.217	0.176	0.041	0.678
12	Se	60	0.683	0.354	0.091	0.865
13	Se	60	0.277	0.16	0.067	1.34
14	Se	14.137	0.42	0.088	0.166	0.151
15	Se	54.985	0.149	0.182	0.092	0.641

Phasing MAD shell

Resolution (Å)	FOM	Reflection
7.31-50	0.52	3879
4.6-7.31	0.47	6877
3.59-4.6	0.49	8754
3.04-3.59	0.47	10255
2.68-3.04	0.35	11480
2.43-2.68	0.23	12326
2.23-2.43	0.15	13042
2.08-2.23	0.09	12453

Phasing dm

FOM : 0.54 / FOM acentric: 0.54 / FOM centric: 0.62 / Reflection: 82520 / Reflection acentric: 77548 / Reflection centric: 4972

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.6-40.315	0.95	0.95	0.92	4047	3389	658
3.5-5.6	0.94	0.94	0.91	12195	11083	1112
2.8-3.5	0.81	0.82	0.76	15100	14112	988
2.4-2.8	0.56	0.56	0.48	14922	14142	780
2.1-2.4	0.3	0.3	0.25	25194	24133	1061
2-2.1	0.13	0.13	0.14	11062	10689	373

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.08	phasing
RESOLVE	2.08	phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.96→10 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.926 / SU B: 5.472 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26292	4086	5 %	RANDOM
R_work	0.21098	-	-	-
obs	0.2136	77725	100 %	-

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: 44.138 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.68 Å²	0 Å²	0 Å²
2-	-	1.56 Å²	0 Å²
3-	-	-	-2.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7934	0	434	277	8645

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	8534
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.354	1.996	11492
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.943	5	989
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.529	22.806	392
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.095	15	1385
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.437	15	77
X-RAY DIFFRACTION	r_chiral_restr	0.161	0.2	1219
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6343
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.25	0.2	3920
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.327	0.2	5657
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	447
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.198	0.2	47
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.123	0.2	10
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.55	1.5	5049
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.305	2	7884
X-RAY DIFFRACTION	r_scbond_it	3.291	3	4068
X-RAY DIFFRACTION	r_scangle_it	4.923	4.5	3608
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3920 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.36	0.5
medium thermal	0.85	2

LS refinement shell

Resolution: 1.96→2.008 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	149	-
R_work	0.28	2841	-
obs	-	-	100 %

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