PDB-9ulx: crystal structure of apo AbGHMP

ID or keywords:

Entry

Database: PDB / ID: 9ulx

Title

crystal structure of apo AbGHMP

Components

AbGHMP

Keywords

TRANSFERASE / arabinokinase

Function / homology

ACETATE ION

Function and homology information

Biological species

Acidobacteriota (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.16 Å

Authors

He, C. / Li, F.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: crystal structure of apo AbGHMP
Authors: He, C. / Li, F.

History

Deposition	Apr 21, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ulx.cif.gz	552.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ulx.ent.gz	460.4 KB	Display	PDB format
PDBx/mmJSON format	9ulx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/9ulx ftp://data.pdbj.org/pub/pdb/validation_reports/ul/9ulx	HTTPS FTP

-
Related structure data

Related structure data	9ulyC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AbGHMP

B: AbGHMP

C: AbGHMP

hetero molecules

162 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AbGHMP

B: AbGHMP

C: AbGHMP

hetero molecules

A: AbGHMP

B: AbGHMP

C: AbGHMP

hetero molecules

defined by author&software
Evidence: gel filtration
323 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.840, 143.177, 194.198
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-632- HOH

#1: Protein	AbGHMP Mass: 53874.707 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Author state: The sequence are available in the NCBI GenBank. The relevant link is: https://www.ncbi.nlm.nih.gov/protein/MBS1788809.1/. Source: (gene. exp.) Acidobacteriota (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris at pH 6.5, 16% (w/v) polyethylene glycol (PEG) 10,000, and 5 mM MgCl2

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 2.16→94.52 Å / Num. obs: 88618 / % possible obs: 94.3 % / Redundancy: 11.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.033 / R_rim(I) all: 0.115 / Χ²: 0.94 / Net I/σ(I): 15.6 / Num. measured all: 1042528
Reflection shell	Resolution: 2.16→2.28 Å / % possible obs: 90.8 % / Redundancy: 11.6 % / R_merge(I) obs: 1.202 / Num. measured all: 143792 / Num. unique obs: 12364 / CC_1/2: 0.803 / R_pim(I) all: 0.363 / R_rim(I) all: 1.257 / Χ²: 0.84 / Net I/σ(I) obs: 2.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
Aimless		data scaling
PDB_EXTRACT		data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.16→62.92 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2216	4402	4.97 %
R_work	0.186	-	-
obs	0.1878	88542	94.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.16→62.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10880	0	8	318	11206

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11116
X-RAY DIFFRACTION	f_angle_d	0.814	15094
X-RAY DIFFRACTION	f_dihedral_angle_d	13.483	3996
X-RAY DIFFRACTION	f_chiral_restr	0.05	1682
X-RAY DIFFRACTION	f_plane_restr	0.008	1993

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 (%)
2.16-2.18	0.3182	148	0.2732	2921	X-RAY DIFFRACTION	100
2.18-2.21	0.2886	158	0.2546	2971	X-RAY DIFFRACTION	100
2.21-2.24	0.2604	136	0.2477	2936	X-RAY DIFFRACTION	100
2.24-2.26	0.3137	92	0.268	1780	X-RAY DIFFRACTION	60
2.26-2.29	0.2908	159	0.237	2919	X-RAY DIFFRACTION	100
2.29-2.33	0.2949	162	0.2245	2976	X-RAY DIFFRACTION	100
2.33-2.36	0.2497	148	0.2223	2907	X-RAY DIFFRACTION	100
2.36-2.39	0.2449	160	0.2158	2969	X-RAY DIFFRACTION	100
2.39-2.43	0.2637	140	0.2139	2992	X-RAY DIFFRACTION	100
2.43-2.47	0.2456	151	0.214	2936	X-RAY DIFFRACTION	100
2.47-2.51	0.2801	139	0.213	2998	X-RAY DIFFRACTION	100
2.51-2.56	0.2367	152	0.2035	2934	X-RAY DIFFRACTION	100
2.56-2.61	0.2855	148	0.2048	2932	X-RAY DIFFRACTION	100
2.61-2.65	0.2622	151	0.2133	2454	X-RAY DIFFRACTION	99
2.68-2.72	0.2217	109	0.2232	2221	X-RAY DIFFRACTION	96
2.72-2.78	0.25	163	0.203	2910	X-RAY DIFFRACTION	100
2.78-2.85	0.2601	159	0.2034	2972	X-RAY DIFFRACTION	100
2.85-2.93	0.2375	168	0.212	2954	X-RAY DIFFRACTION	100
2.93-3.02	0.2676	155	0.2104	2952	X-RAY DIFFRACTION	100
3.02-3.11	0.2383	162	0.2027	2970	X-RAY DIFFRACTION	100
3.11-3.23	0.2371	157	0.2047	2976	X-RAY DIFFRACTION	100
3.23-3.35	0.227	150	0.19	2970	X-RAY DIFFRACTION	100
3.35-3.51	0.2176	98	0.1981	2073	X-RAY DIFFRACTION	69
3.51-3.69	0.2291	109	0.1927	2218	X-RAY DIFFRACTION	75
3.69-3.92	0.1961	109	0.1828	2111	X-RAY DIFFRACTION	70
3.92-4.23	0.1762	172	0.1554	2973	X-RAY DIFFRACTION	100
4.23-4.65	0.1811	166	0.148	2989	X-RAY DIFFRACTION	100
4.65-5.32	0.192	158	0.1575	3038	X-RAY DIFFRACTION	100
5.32-6.71	0.2327	157	0.1885	3045	X-RAY DIFFRACTION	100
6.71-62.92	0.1893	166	0.1494	3143	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.6136	-0.0609	-0.1184	1.3132	0.5708	2.0187	-0.0976	-0.387	0.0684	0.4493	-0.1541	0.3714	-0.1018	-0.2284	0.0462	0.5261	-0.0554	0.0549	0.3989	-0.0274	0.2903	-8.5111	-46.0771	-12.8235
2	1.394	-0.9057	-0.5655	2.7611	0.4701	2.6838	-0.0715	-0.6953	-0.3968	0.9692	0.0079	0.0959	0.4304	-0.0362	0.0209	0.7665	-0.1087	-0.0077	0.6492	0.0817	0.3742	-2.3278	-60.0293	-2.6186
3	2.0927	0.1682	-0.3286	2.2055	-0.1798	2.2858	0.01	-0.3137	-0.1431	0.344	-0.0261	0.0047	0.0636	-0.0035	0.0171	0.4851	-0.0691	-0.0323	0.4422	0.0418	0.2642	1.1967	-54.9526	-12.2175
4	2.3983	-0.6677	-0.017	1.5049	0.5283	1.0678	0.0214	-0.1764	-0.2146	0.061	-0.0502	-0.0592	0.0959	0.1669	0.0331	0.316	-0.0249	-0.0214	0.2766	0.0613	0.2191	5.651	-64.6535	-34.5503
5	2.8819	-0.6894	-0.0048	1.6755	-0.7372	2.9377	-0.0071	0.0983	0.2455	-0.2439	-0.1063	-0.2277	-0.0073	-0.0882	0.1132	0.2655	0.0068	-0.0316	0.2414	-0.0207	0.2078	-7.8827	-54.729	-44.7795
6	1.224	-0.1026	0.2881	1.2459	0.1968	1.2472	0.0463	-0.1889	-0.0072	0.0709	-0.1274	0.315	-0.0163	-0.1935	0.1078	0.2807	-0.0233	0.0243	0.2889	-0.0139	0.2506	-15.9798	-53.1025	-30.8929
7	1.6022	0.8378	-1.3697	1.9835	-0.7441	3.634	0.1661	-0.3389	-0.0973	0.4093	0.1759	0.0789	0.2172	-0.31	-0.2974	0.5192	-0.078	-0.0383	0.6563	0.2504	0.5551	11.413	-22.3766	-0.3898
8	2.8495	-0.042	-1.0055	3.8508	-0.868	4.0064	-0.0346	-0.3952	-0.1607	0.4886	0.2243	-0.1375	0.0145	0.2687	-0.1513	0.6583	-0.0197	-0.0881	0.7796	0.1212	0.5854	25.4034	-17.9992	4.1405
9	0.4064	-0.2544	-0.8691	1.1409	0.4218	3.4488	-0.0324	-0.2121	-0.0777	0.1702	0.2871	0.1992	-0.0118	-0.2044	-0.258	0.4177	-0.0518	-0.0242	0.541	0.1675	0.5884	17.9303	-16.6255	-12.8444
10	2.2481	0.4911	-0.3966	3.436	-2.2084	2.6529	0.0848	-0.2705	-0.3255	-0.0659	0.086	0.1783	0.273	-0.0672	0.0342	0.3234	-0.0682	-0.0134	0.3082	0.0595	0.3316	29.0717	-19.5857	-27.0277
11	1.6793	-1.0968	-0.1966	3.1937	0.7089	2.7698	-0.0955	-0.2703	-0.1395	0.1697	0.052	0.3055	-0.0006	-0.1679	0.0962	0.3859	-0.0801	0.0444	0.6338	0.3566	0.7425	8.2207	-24.8364	-5.7969
12	1.2536	-0.2711	0.7746	1.8286	0.0014	2.7959	-0.0424	0.2494	0.0401	-0.4898	0.0101	0.0503	-0.2947	-0.2485	0.0653	0.4828	-0.0739	-0.1063	0.4792	0.103	0.5667	9.978	-6.5802	-73.3522
13	2.8006	-0.8479	-0.6529	4.1213	0.6335	4.4828	-0.0595	0.1829	0.0702	-0.8211	0.0068	-0.4851	0.0681	0.2531	0.0984	0.8164	-0.0994	0.1008	0.5568	0.0848	0.4871	21.0749	-17.1718	-85.0971
14	0.7461	0.8226	0.6028	2.1389	-0.2594	2.3259	-0.035	0.1144	0.0197	-0.5325	-0.0635	0.0305	0.1804	-0.2039	0.1002	0.3918	-0.0813	-0.0788	0.4164	0.0743	0.503	13.9211	-16.8752	-68.7402
15	0.411	1.2828	-0.641	2.5119	0.1473	0.8438	-0.0265	-0.0752	-0.5049	-0.0597	-0.0277	-1.1804	0.2664	0.2174	-0.0257	0.3232	-0.005	-0.149	0.3501	0.0944	0.9185	33.6229	-28.4632	-53.5616
16	1.837	0.4446	0.443	1.4049	-0.1206	1.3513	0.1642	-0.0315	-0.0373	0.0753	-0.0789	-0.0945	-0.0493	-0.128	-0.0985	0.2615	-0.0425	-0.0668	0.2835	0.0617	0.451	21.287	-6.4205	-50.7106

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 71 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 72 through 126 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 127 through 221 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 222 through 374 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 375 through 402 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 403 through 488 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 91 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 92 through 169 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 170 through 264 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 265 through 463 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 464 through 488 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 79 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 80 through 146 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 147 through 246 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 247 through 351 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 352 through 487 )

-
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