PDB-7cb5: The 6-phosphogluconate dehydrogenase from Staphylococcus aureus (...

ID or keywords:

Entry

Database: PDB / ID: 7cb5

Title

The 6-phosphogluconate dehydrogenase from Staphylococcus aureus (6-phosphogluconate bound)

Components

6-phosphogluconate dehydrogenase, decarboxylating

Keywords

CYTOSOLIC PROTEIN /

Pentose phosphate pathway / decarboxylating

Function / homology

Function and homology information

phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) /

phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch /

NADP binding /

cytosol
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.54 Å

Authors

Wang, H. / Wang, M. / Sun, H.

Funding support

Hong Kong,

China, 2items

Citation

Journal: Nat Commun / Year: 2021
Title: Multi-target mode of action of silver against Staphylococcus aureus endows it with capability to combat antibiotic resistance.
Authors: Wang, H. / Wang, M. / Xu, X. / Gao, P. / Xu, Z. / Zhang, Q. / Li, H. / Yan, A. / Kao, R.Y. / Sun, H.

History

Deposition	Jun 10, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 23, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7cb5.cif.gz	809.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7cb5.ent.gz	602 KB	Display	PDB format
PDBx/mmJSON format	7cb5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/7cb5 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cb5	HTTPS FTP

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Related structure data

Related structure data	7cb0C 7cb6C 7bc0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2zya-d 7cb0-2 7cb0-1 1pgp-1 5uq9-3 6fqy-d 2pgd-1 1pgq-1 3fwn-d 2zyg-1 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	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 6-phosphogluconate dehydrogenase, decarboxylating

B: 6-phosphogluconate dehydrogenase, decarboxylating

C: 6-phosphogluconate dehydrogenase, decarboxylating

D: 6-phosphogluconate dehydrogenase, decarboxylating

hetero molecules

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

1

A: 6-phosphogluconate dehydrogenase, decarboxylating

B: 6-phosphogluconate dehydrogenase, decarboxylating

hetero molecules

defined by author&software
Evidence: gel filtration
104 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 6-phosphogluconate dehydrogenase, decarboxylating

D: 6-phosphogluconate dehydrogenase, decarboxylating

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.920, 132.620, 169.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	6-phosphogluconate dehydrogenase, decarboxylating / Mass: 51857.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Newman) (bacteria) Gene: gnd, NWMN_1417 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3KGN1, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar	ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID / 6-Phosphogluconic acid Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₆H₁₃O₁₀P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.5 Å³/Da / Density % sol: 50.71 % / Description: Transparent block-like small crystals
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M NaNO3, 0.2M NH4NO3, 0.1M MES-Na, 22% PEG 3350 / PH range: 6.0-6.5 / Temp details: room temperature

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: Nitrogen Flow / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2018

Radiation

Monochromator: graphite filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.54→80.84 Å / Num. obs: 69146 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.113 / R_pim(I) all: 0.032 / R_rim(I) all: 0.117 / Net I/σ(I): 18.5 / Num. measured all: 931049 / Scaling rejects: 16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.54-2.61	13.9	1.33	70425	5067	0.814	0.368	1.381	2.1	100
11.36-80.84	11.9	0.03	10541	885	0.999	0.009	0.032	58.6	99.7

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Processing

Software

Name	Version	Classification
Aimless	0.7.2	data scaling
PHENIX	1.18.1	refinement
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7BC0

7bc0

Resolution: 2.54→69.03 Å / SU ML: 0.3006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2409	3485	5.05 %
R_work	0.1994	65557	-
obs	0.2015	69042	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 71.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.54→69.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14330	0	68	131	14529

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	14649
X-RAY DIFFRACTION	f_angle_d	0.5473	19799
X-RAY DIFFRACTION	f_chiral_restr	0.0391	2192
X-RAY DIFFRACTION	f_plane_restr	0.003	2571
X-RAY DIFFRACTION	f_dihedral_angle_d	22.663	5388

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 (%)
2.54-2.57	0.3031	149	0.3047	2584	X-RAY DIFFRACTION	99.96
2.57-2.61	0.3606	137	0.2929	2574	X-RAY DIFFRACTION	99.82
2.61-2.65	0.3546	149	0.2899	2573	X-RAY DIFFRACTION	99.96
2.65-2.69	0.3537	139	0.2879	2615	X-RAY DIFFRACTION	99.75
2.69-2.74	0.3398	133	0.2913	2580	X-RAY DIFFRACTION	99.85
2.74-2.78	0.332	132	0.2768	2615	X-RAY DIFFRACTION	99.93
2.78-2.83	0.3102	130	0.2676	2583	X-RAY DIFFRACTION	99.89
2.83-2.89	0.2857	148	0.2621	2585	X-RAY DIFFRACTION	99.38
2.89-2.95	0.2641	139	0.2617	2594	X-RAY DIFFRACTION	99.82
2.95-3.01	0.284	133	0.2591	2586	X-RAY DIFFRACTION	99.85
3.01-3.08	0.2879	136	0.2559	2621	X-RAY DIFFRACTION	99.82
3.08-3.16	0.2606	134	0.2545	2608	X-RAY DIFFRACTION	99.85
3.16-3.24	0.3184	122	0.2449	2605	X-RAY DIFFRACTION	99.89
3.24-3.34	0.2529	132	0.2314	2631	X-RAY DIFFRACTION	99.86
3.34-3.45	0.2626	149	0.2224	2587	X-RAY DIFFRACTION	99.93
3.45-3.57	0.2445	140	0.2035	2621	X-RAY DIFFRACTION	100
3.57-3.71	0.2795	143	0.2116	2640	X-RAY DIFFRACTION	100
3.71-3.88	0.2612	154	0.1856	2585	X-RAY DIFFRACTION	100
3.88-4.09	0.1939	124	0.1684	2642	X-RAY DIFFRACTION	99.75
4.09-4.34	0.2239	157	0.1623	2619	X-RAY DIFFRACTION	99.46
4.34-4.68	0.1857	153	0.1528	2616	X-RAY DIFFRACTION	100
4.68-5.15	0.2294	148	0.1607	2677	X-RAY DIFFRACTION	99.96
5.15-5.89	0.2353	124	0.1922	2688	X-RAY DIFFRACTION	100
5.89-7.42	0.2046	134	0.1818	2723	X-RAY DIFFRACTION	100
7.42-69.03	0.1628	146	0.1486	2805	X-RAY DIFFRACTION	98.73

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	2.45013609744	0.630343567402	0.202916342556	2.84861636609	-0.412633533297	3.23049339197	-0.0466185998324	-0.246955988301	-0.0377132481656	0.536061161429	-0.0542932572376	0.568235745784	0.144131391116	-0.437529019036	0.091686829734	0.603782750417	-0.00521152058978	0.167056052922	0.395694336938	-0.0540940160764	0.466460879743	-7.74664232674	-53.9176680315	-15.5007751692
2	0.541222383989	-0.577476509265	0.315702966934	1.58421568885	-0.425890702935	2.47292905714	0.121083421052	0.172814515809	-0.235028960989	-0.288891474093	-0.11775931904	0.272041874767	0.573456610206	-0.177909296507	0.0785713838736	0.481050914036	0.0147393062595	-0.0239414113304	0.421450464006	-0.0683988454523	0.396479019545	-1.90215678954	-47.7430590428	-40.260015352
3	2.2959533175	-0.237625684902	0.813192008543	2.19731538739	0.252508001177	2.09259702527	-0.0209909312417	0.21034064799	0.236526190123	-0.241674152006	-0.178446985571	0.36276695777	-0.0247455482852	-0.360706986347	0.103247909507	0.391153881575	0.0177281997488	-0.0442513560147	0.379915288943	-0.0358181667547	0.36814430783	-6.11161518301	-29.9572756072	-42.3300620759
4	1.12694135718	-0.183851418186	0.262358844389	1.81356360535	-0.0726393061539	1.38809543054	0.086330414753	0.183190948509	0.0667752738313	-0.148512785822	-0.11057261958	-0.314577980036	0.0357923758394	0.247560584892	0.0355553698893	0.457705029947	0.0655294711007	0.00777495269304	0.486735548475	0.00891514270258	0.392676475441	14.642693144	-37.4663680857	-42.6645510414
5	3.27287562907	0.902978220914	1.93872463415	3.53837839504	1.0066826286	5.47022645551	-0.194468214237	-0.241218308282	0.465940930438	0.224182115916	-0.123757758874	-0.299572318873	-0.3754537565	0.235797263079	0.284672629971	0.387501665068	0.00985326398041	-0.109672754884	0.385765877832	-0.0568925957223	0.590867705188	17.1177558985	-5.38567563338	-11.2777518957
6	1.46144522851	0.0150644061568	0.616595000741	1.92342754311	0.850463999718	2.30212725745	-0.0885613938447	0.389867905724	0.500513817483	-0.486581322726	4.58196008604E-5	-0.317021051923	-0.451194001036	0.387562201936	0.115103668176	0.616419523399	-0.0658044921832	-0.0201006461497	0.560984455778	0.18031041215	0.647168237199	18.832607713	-12.1700762193	-42.3435623496
7	2.29101703476	0.303216770417	-0.352251642635	2.62068231076	0.136923949545	1.65073155553	0.0858896041206	0.21360364049	0.0740212751363	-0.176026614383	-0.106379954802	-0.484733942746	-0.0949697950731	0.385516830908	0.00514364798085	0.497655568582	0.0215250726356	-0.0394425789272	0.495968039529	0.0950967014	0.541284058993	20.0397868073	-25.4193776318	-40.3927530193
8	1.1765465729	-0.0547024107269	0.305876098729	1.93693338448	0.680932345407	1.5451193919	-0.0895007925783	-0.0032061389211	0.287980858355	-0.22671972331	-0.206248143116	0.263960403981	-0.279445064134	-0.113908499821	0.282519610172	0.524972738171	0.0511814615705	-0.117543291419	0.41013875876	0.0464720951854	0.466466855395	-0.476417435561	-17.7348020363	-41.7216812133
9	2.92746718414	0.27909852579	0.336568838102	3.3298457176	0.492514346939	2.5975534917	0.00301803783296	-0.0140371898956	-0.307718946812	0.217794524841	-0.0739720736324	-0.866047008197	-0.0510650529752	0.850818389689	0.0325721460565	0.450609681582	0.0104243689782	-0.0283628492779	0.739099316407	0.128585734073	0.616985254566	-6.19983300474	-19.2721456074	24.9167202276
10	1.21282970719	1.63442481303	-0.0181763197479	7.54006095526	0.947875680742	0.347372940677	0.331388894317	-0.221314733589	0.269766818662	1.26312690653	-0.165234645212	-0.259713309291	-0.287983854461	0.256889653734	-0.173257551143	0.863269086247	-0.192990714663	0.00335731671245	0.686945627835	-0.0432522789358	0.511260482995	-8.33765909804	11.9263483783	21.836591688
11	2.60304382332	1.57256789444	0.270161620743	3.16294471552	0.397550103083	2.27401761688	0.215202701947	0.0306564696384	0.107758559852	0.471515442325	-0.0164467003677	-0.260196626661	-0.298223696617	0.281512044984	-0.201074349943	0.506919855979	-0.078321558275	0.0398154767345	0.409863263644	-0.0145170013801	0.412868248179	-11.1777208716	11.3161377412	12.2856134682
12	1.02768557391	-0.924003832104	-0.759546679398	4.18323882765	-1.84045111896	2.35345955849	0.205635457243	-0.11546936682	0.20697821276	1.34865736511	-0.109451849543	0.183374062713	-0.557549714991	0.115565370509	-0.0837387635329	0.855592048522	-0.11278821	0.110863924324	0.476560858386	-0.00272520392046	0.485706230309	-24.0974731941	0.363419860229	26.4696633055
13	2.21537226628	0.958559509946	0.517513906984	2.55851595284	-0.0100531861156	2.61735994175	0.0204400014181	0.198014529679	0.610629055244	-0.018966049502	0.0501548340004	0.540941678309	-0.481500359898	-0.283469895861	-0.0160662755433	0.645675677332	0.0441559862483	0.148163767056	0.448594626676	0.0831067498366	0.662018946215	-31.4355262371	14.6916141074	5.63618206
14	3.91686859772	0.246582976232	0.948355601771	1.02496379041	0.078877199787	1.70630086409	0.309601172655	0.248454453796	-1.16561204187	-0.685886686084	0.424069574545	1.56728932023	0.89414101696	-0.391131390168	-0.572506141912	0.827078959981	-0.23761396795	-0.28011647558	0.820882123069	0.0574592091767	1.30253013665	-29.0701240527	-12.0766122728	-24.170692497
15	1.20077383117	0.332714164544	0.447676118803	1.62617464301	0.689346087953	2.181313394	-0.0577987336428	0.356977655382	0.300969298016	-0.268061656595	0.111225218897	0.406185433472	-0.497901980358	-0.212049142473	-0.0568230135845	0.593987097396	0.00453150435751	0.0705958593158	0.586739280429	0.188504529703	0.62479610291	-28.6210185381	11.5594408374	-7.93969851525
16	2.03490073697	0.807912577764	-0.0251855315559	2.29127294681	0.177152933995	2.53398360738	-0.0351256182653	0.405832309628	0.217499108741	-0.281630966159	0.117807249465	-0.0730609167292	-0.5449923107	0.480230336738	-0.0638827193327	0.599014107272	-0.143665672959	0.118746620037	0.620903611983	0.0688300607034	0.497474391732	-10.7424998923	14.4668985972	-3.45494787635

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 144 )	A	A	1 - 144	1 - 144
2	2	chain 'A' and (resid 145 through 239 )	A	A	145 - 239	145 - 239
3	3	chain 'A' and (resid 240 through 312 )	A	A	240 - 312	240 - 312
4	4	chain 'A' and (resid 313 through 466 )	A	A	313 - 466	313 - 466
5	5	chain 'B' and (resid 1 through 174 )	B	C	1 - 174	1 - 174
6	6	chain 'B' and (resid 175 through 239 )	B	C	175 - 239	175 - 239
7	7	chain 'B' and (resid 240 through 312 )	B	C	240 - 312	240 - 312
8	8	chain 'B' and (resid 313 through 467 )	B	C	313 - 467	313 - 467
9	9	chain 'C' and (resid 1 through 174 )	C	E	1 - 174	1 - 174
10	10	chain 'C' and (resid 175 through 239 )	C	E	175 - 239	175 - 239
11	11	chain 'C' and (resid 240 through 346 )	C	E	240 - 346	240 - 346
12	12	chain 'C' and (resid 347 through 389 )	C	E	347 - 389	347 - 389
13	13	chain 'C' and (resid 390 through 466 )	C	E	390 - 466	390 - 466
14	14	chain 'D' and (resid 4 through 144 )	D	G	4 - 144	1 - 141
15	15	chain 'D' and (resid 145 through 312 )	D	G	145 - 312	142 - 309
16	16	chain 'D' and (resid 313 through 467 )	D	G	313 - 467	310 - 464

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About Yorodumi

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Yorodumi