PDB-9ij6: Crystal structure of the complex of erythrose-4-phosphate dehydro...

ID or keywords:

Entry

Database: PDB / ID: 9ij6

Title

Crystal structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with Adenosine phosphate at 2.40 A resolution.

Components

Glyceraldehyde-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

Function and homology information

Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P.

Funding support

India, 2items

Citation

Journal: To Be Published
Title: Crystal structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with Adenosine phosphate at 2.40 A resolution.
Authors: Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Jeyakanthan, J. / Sharma, S. / Raje, C.I. / Singh, T.P.

History

Deposition	Jun 21, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ij6.cif.gz	302.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9ij6_validation.pdf.gz	4.3 MB	Display	wwPDB validaton report
Full document	9ij6_full_validation.pdf.gz	4.3 MB	Display
Data in XML	9ij6_validation.xml.gz	55.7 KB	Display
Data in CIF	9ij6_validation.cif.gz	79.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ij/9ij6 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/9ij6	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	#50 - Feb 2004 Glycolytic Enzymes similarity (9) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

154 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	147.578, 167.012, 155.058
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 38062.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_ ...Gene: epd, gap, A7M90_08740, Aba7835_13565, ABCAM1_1226, ABR2091_1144, APD17_19525, AYR68_05750, B7L45_13105, B9W25_17760, C2U32_02225, CAS83_00220, CBL15_12235, CTZ19_12640, D8O08_008145, DLI71_18430, EA706_09520, EA720_004470, EGM95_14355, F4T85_07645, FDN00_13975, FE003_13215, FJU42_18405, FJV09_11310, GSE42_06795, HBK86_03865, IAG11_16195, SAMEA4394745_03679 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A059ZTK9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.14 Å³/Da / Density % sol: 60.8 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.2M MgSO4.6H2O, 0.1M HEPES sodium (pH 7.5)

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 2.4→83.646 Å / Num. obs: 74905 / % possible obs: 100 % / Redundancy: 9.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.214 / R_pim(I) all: 0.071 / R_rim(I) all: 0.227 / Net I/σ(I): 7.6
Reflection shell	Resolution: 2.4→2.45 Å / Redundancy: 9.2 % / R_merge(I) obs: 2.05 / Mean I/σ(I) obs: 1 / Num. unique obs: 4617 / CC_1/2: 0.6 / R_pim(I) all: 0.7 / R_rim(I) all: 2.17 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→83.646 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.949 / SU B: 9.873 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.265 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2196	1111	1.484 %
R_work	0.1696	73757	-
all	0.17	-	-
obs	-	74868	99.944 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 50.406 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.61 Å²	0 Å²	-0 Å²
2-	-	-4.743 Å²	0 Å²
3-	-	-	5.353 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→83.646 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10717	0	122	692	11531

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	11083
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10547
X-RAY DIFFRACTION	r_angle_refined_deg	1.527	1.795	15091
X-RAY DIFFRACTION	r_angle_other_deg	0.509	1.762	24191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.15	5	1366
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.636	5	71
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.17	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.672	10	1861
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.334	10	507
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1773
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	12997
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2527
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	2139
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	9871
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	5311
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	6021
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	541
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.117	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.132	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.089	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	3.962	5.015	5461
X-RAY DIFFRACTION	r_mcbond_other	3.954	5.015	5461
X-RAY DIFFRACTION	r_mcangle_it	5.889	8.999	6822
X-RAY DIFFRACTION	r_mcangle_other	5.889	9	6823
X-RAY DIFFRACTION	r_scbond_it	5.213	5.71	5622
X-RAY DIFFRACTION	r_scbond_other	5.213	5.708	5618
X-RAY DIFFRACTION	r_scangle_it	8.25	10.2	8267
X-RAY DIFFRACTION	r_scangle_other	8.251	10.195	8262
X-RAY DIFFRACTION	r_lrange_it	10.192	47.178	12111
X-RAY DIFFRACTION	r_lrange_other	10.189	47.222	12014

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.4-2.462	0.398	92	0.338	5418	0.339	5512	0.854	0.886	99.9637	0.328
2.462-2.53	0.35	76	0.31	5269	0.311	5347	0.907	0.911	99.9626	0.298
2.53-2.603	0.246	75	0.288	5107	0.287	5184	0.923	0.93	99.9614	0.274
2.603-2.683	0.348	64	0.262	4991	0.263	5058	0.925	0.943	99.9407	0.244
2.683-2.771	0.32	72	0.237	4829	0.239	4904	0.929	0.955	99.9388	0.217
2.771-2.868	0.309	70	0.222	4660	0.224	4731	0.941	0.962	99.9789	0.201
2.868-2.976	0.257	63	0.19	4536	0.191	4599	0.962	0.973	100	0.167
2.976-3.098	0.232	65	0.181	4355	0.182	4421	0.958	0.976	99.9774	0.158
3.098-3.235	0.225	60	0.175	4180	0.176	4240	0.965	0.979	100	0.157
3.235-3.393	0.263	60	0.159	3979	0.16	4040	0.95	0.984	99.9752	0.143
3.393-3.576	0.156	43	0.145	3830	0.145	3875	0.981	0.988	99.9484	0.134
3.576-3.792	0.195	54	0.14	3597	0.141	3651	0.976	0.989	100	0.129
3.792-4.054	0.176	49	0.132	3400	0.132	3450	0.978	0.989	99.971	0.122
4.054-4.378	0.194	57	0.125	3154	0.127	3211	0.977	0.991	100	0.119
4.378-4.794	0.183	42	0.11	2927	0.111	2971	0.984	0.993	99.9327	0.107
4.794-5.358	0.195	59	0.125	2647	0.127	2706	0.977	0.991	100	0.118
5.358-6.182	0.193	26	0.173	2387	0.173	2414	0.971	0.984	99.9586	0.16
6.182-7.562	0.185	42	0.162	1985	0.162	2028	0.98	0.985	99.9507	0.153
7.562-10.65	0.149	31	0.119	1581	0.119	1613	0.986	0.992	99.938	0.121
10.65-83.646	0.2	11	0.211	925	0.21	953	0.968	0.968	98.2162	0.201

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