PDB-8zoz: Crystal structure of the complex of glyceraldehyde-3-phosphate de...

ID or keywords:

Entry

Database: PDB / ID: 8zoz

Title

Crystal structure of the complex of glyceraldehyde-3-phosphate dehydrogenase of type B from Acinetobacter baumannii with Adenosine monophosphate at 3.20 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: 3.2 Å

Authors

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

Funding support

India, 2items

Citation

Journal: To Be Published
Title: Crystal structure of the complex of glyceraldehyde-3-phosphate dehydrogenase of type B from Acinetobacter baumannii with Adenosine monophosphate at 3.20 A resolution.
Authors: Pahuja, P. / Viswanathan, V. / Kumari, A. / Singh, A. / Kumar, A. / Sharma, P. / Chopra, S. / Sharma, S. / Raje, C.I. / Singh, T.P.

History

Deposition	May 29, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8zoz.cif.gz	287.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8zoz.ent.gz	225.9 KB	Display	PDB format
PDBx/mmJSON format	8zoz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8zoz_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	8zoz_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8zoz_validation.xml.gz	49.5 KB	Display
Data in CIF	8zoz_validation.cif.gz	66.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zo/8zoz ftp://data.pdbj.org/pub/pdb/validation_reports/zo/8zoz	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	147.509, 167.732, 150.726
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-403- SO4

#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.: 6 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.83 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.2M MgSo4. 6H2O, 0.1M HEPES sodium (pH 7.5)

-
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: 3.2→89.26 Å / Num. obs: 30330 / % possible obs: 97.2 % / Redundancy: 12.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.23 / R_pim(I) all: 0.069 / R_rim(I) all: 0.24 / Net I/σ(I): 7.9
Reflection shell	Resolution: 3.2→3.37 Å / Redundancy: 10.9 % / R_merge(I) obs: 2.39 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4487 / CC_1/2: 0.86 / R_pim(I) all: 0.757 / R_rim(I) all: 2.51 / % possible all: 99.7

-
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: 3.2→84.007 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.927 / SU B: 41.213 / SU ML: 0.613 / Cross valid method: FREE R-VALUE / ESU R Free: 0.561
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2793	1202	3.967 %
R_work	0.2012	29101	-
all	0.204	-	-
obs	-	30303	97.181 %

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: 129.269 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	12.992 Å²	0 Å²	-0 Å²
2-	-	-18.822 Å²	-0 Å²
3-	-	-	5.831 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→84.007 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10716	0	122	89	10927

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	11092
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10547
X-RAY DIFFRACTION	r_angle_refined_deg	1.112	1.794	15103
X-RAY DIFFRACTION	r_angle_other_deg	0.402	1.762	24191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.284	5	1366
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.483	5	71
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.853	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.152	10	1861
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.489	10	507
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	1773
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	13011
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2529
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	2311
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	10474
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	5297
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	5761
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	317
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.027	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.148	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.224	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.188	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	7.172	12.78	5467
X-RAY DIFFRACTION	r_mcbond_other	7.172	12.78	5467
X-RAY DIFFRACTION	r_mcangle_it	11.256	22.958	6832
X-RAY DIFFRACTION	r_mcangle_other	11.256	22.959	6833
X-RAY DIFFRACTION	r_scbond_it	7.01	13.562	5625
X-RAY DIFFRACTION	r_scbond_other	7.007	13.561	5621
X-RAY DIFFRACTION	r_scangle_it	11.558	24.663	8271
X-RAY DIFFRACTION	r_scangle_other	11.557	24.662	8266
X-RAY DIFFRACTION	r_lrange_it	15.651	118.855	11985
X-RAY DIFFRACTION	r_lrange_other	15.651	118.873	11985

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
3.2-3.283	0.502	100	0.464	2194	0.465	2300	0.792	0.816	99.7391	0.447
3.283-3.373	0.412	91	0.433	2092	0.432	2192	0.773	0.814	99.5894	0.404
3.373-3.47	0.387	88	0.387	2060	0.387	2155	0.835	0.843	99.6752	0.35
3.47-3.577	0.347	80	0.349	2010	0.349	2097	0.869	0.878	99.6662	0.318
3.577-3.694	0.388	71	0.319	1970	0.322	2048	0.876	0.9	99.6582	0.288
3.694-3.824	0.308	70	0.268	1889	0.269	1960	0.917	0.944	99.949	0.245
3.824-3.968	0.311	38	0.204	1049	0.208	1893	0.924	0.964	57.4221	0.177
3.968-4.129	0.273	81	0.173	1754	0.177	1840	0.95	0.973	99.7283	0.154
4.129-4.312	0.281	81	0.148	1679	0.154	1771	0.943	0.982	99.3789	0.134
4.312-4.522	0.193	59	0.131	1607	0.133	1674	0.968	0.987	99.5221	0.118
4.522-4.766	0.229	67	0.119	1528	0.124	1597	0.963	0.99	99.8748	0.111
4.766-5.054	0.188	62	0.119	1475	0.122	1537	0.974	0.993	100	0.111
5.054-5.402	0.17	48	0.127	1398	0.128	1447	0.98	0.992	99.9309	0.12
5.402-5.833	0.26	59	0.169	1271	0.174	1331	0.958	0.986	99.9249	0.158
5.833-6.386	0.334	43	0.183	1201	0.188	1244	0.933	0.983	100	0.173
6.386-7.135	0.248	43	0.156	1080	0.16	1123	0.963	0.983	100	0.149
7.135-8.229	0.279	45	0.149	964	0.155	1009	0.954	0.985	100	0.15
8.229-10.054	0.222	31	0.128	836	0.131	867	0.973	0.994	100	0.132
10.054-14.118	0.185	27	0.168	657	0.169	685	0.982	0.991	99.854	0.174
14.118-84.007	0.436	18	0.329	387	0.333	410	0.948	0.939	98.7805	0.309

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi