PDB-7cb6: The silver-bound 6-phosphogluconate dehydrogenase from Staphyloco...

ID or keywords:

Entry

Database: PDB / ID: 7cb6

Title

The silver-bound 6-phosphogluconate dehydrogenase from Staphylococcus aureus (strain Newman)

Components

6-phosphogluconate dehydrogenase, decarboxylating

Keywords

CYTOSOLIC PROTEIN /

Pentose phosphate pathway / decarboxylating

Function / homology

Function and homology information

organic acid catabolic process / D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) /

phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt /

NADP binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.64 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	7cb6.cif.gz	804 KB	Display	PDBx/mmCIF format
PDB format	pdb7cb6.ent.gz	595.9 KB	Display	PDB format
PDBx/mmJSON format	7cb6.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/7cb6 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cb6	HTTPS FTP

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Related structure data

Related structure data	7cb0SC 7cb5C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2zyg-2 4gwg-2 5uq9-3 7cb0-2 2iyp-2 7cb0-1 5uq9-4 6fqy-d 2pgd-1 5js1-d 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

210 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
105 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
105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.860, 133.860, 171.320
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: Chemical	ChemComp-AG / SILVER ION / Silver Mass: 107.868 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ag
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.51 Å³/Da / Density % sol: 51.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M NaNO3, 0.2M NH4NO3, 0.1M MES-Na, 50% 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 / Details: direct

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: 2.64→80.27 Å / Num. obs: 62107 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.129 / R_pim(I) all: 0.036 / R_rim(I) all: 0.134 / Net I/σ(I): 18.5 / Num. measured all: 834281 / Scaling rejects: 4

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
2.64-2.71	14.1	1.279	63963	4549	0.796	0.351	1.327	2.3	100
11.81-80.27	11.6	0.03	9279	803	1	0.009	0.031	67.2	99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
Aimless	0.7.2	data scaling
PDB_EXTRACT	3.25	data extraction
xia2	2	data reduction
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7CB0

7cb0

Resolution: 2.64→62.34 Å / SU ML: 0.3303 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2463	3128	5.05 %
R_work	0.2037	58857	-
obs	0.2059	61985	99.78 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.64→62.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14280	0	20	54	14354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14536
X-RAY DIFFRACTION	f_angle_d	0.4484	19654
X-RAY DIFFRACTION	f_chiral_restr	0.0371	2169
X-RAY DIFFRACTION	f_plane_restr	0.0022	2569
X-RAY DIFFRACTION	f_dihedral_angle_d	20.7664	5312

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 (%)
2.64-2.68	0.3019	132	0.2714	2689	X-RAY DIFFRACTION	99.93
2.68-2.73	0.3349	138	0.2715	2620	X-RAY DIFFRACTION	99.89
2.73-2.77	0.3608	129	0.2683	2650	X-RAY DIFFRACTION	99.78
2.77-2.82	0.2942	146	0.2773	2630	X-RAY DIFFRACTION	99.93
2.82-2.88	0.3195	168	0.263	2595	X-RAY DIFFRACTION	99.89
2.88-2.94	0.3535	127	0.2452	2685	X-RAY DIFFRACTION	99.93
2.94-3	0.3184	139	0.2446	2647	X-RAY DIFFRACTION	99.82
3-3.07	0.3527	158	0.2569	2613	X-RAY DIFFRACTION	99.75
3.07-3.15	0.2928	138	0.2479	2660	X-RAY DIFFRACTION	99.79
3.15-3.23	0.3023	146	0.2395	2660	X-RAY DIFFRACTION	99.68
3.23-3.33	0.2792	108	0.2351	2677	X-RAY DIFFRACTION	99.89
3.33-3.43	0.279	141	0.2366	2647	X-RAY DIFFRACTION	99.61
3.43-3.56	0.2674	135	0.2287	2678	X-RAY DIFFRACTION	99.96
3.56-3.7	0.249	155	0.2097	2645	X-RAY DIFFRACTION	99.79
3.7-3.87	0.2313	133	0.1936	2679	X-RAY DIFFRACTION	99.72
3.87-4.07	0.1945	136	0.177	2677	X-RAY DIFFRACTION	99.61
4.07-4.33	0.1975	166	0.1709	2673	X-RAY DIFFRACTION	99.86
4.33-4.66	0.2018	161	0.1641	2661	X-RAY DIFFRACTION	99.86
4.66-5.13	0.2192	137	0.1799	2717	X-RAY DIFFRACTION	99.41
5.13-5.87	0.3026	130	0.2086	2725	X-RAY DIFFRACTION	99.86
5.87-7.39	0.2151	144	0.1968	2762	X-RAY DIFFRACTION	100
7.39-62.34	0.1963	161	0.1646	2867	X-RAY DIFFRACTION	99.41

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	4.89366632934	0.938308111525	-1.19264153852	2.48143290571	0.0647223106866	3.71652673723	-0.0714532189594	-0.211854298519	-0.0943582429212	0.0288361156748	-0.0510396261494	0.203290520707	0.129602732624	-0.393693739117	0.127105724594	0.353098187419	0.0146424501287	0.0109636288436	0.444733560215	0.00657472115833	0.371437170829	-16.9783789667	7.70654501061	-11.6197763702
2	1.64796828181	-0.298007540976	0.3882863182	1.18305585674	0.649385408334	1.47330165327	0.0515097634232	0.177991845446	-0.111251602355	-0.171979636445	-0.319177079822	0.237471150851	0.254558406336	-0.405224783681	0.0659568417828	0.50972586301	-0.0290738150665	-0.0469524377382	0.590565406212	-0.135387007705	0.502093766504	-16.8453605574	12.1484580766	-43.9781718419
3	1.34102329106	0.0320958425958	0.10985803297	1.6103431079	-0.0634758906095	1.30917527555	0.0703622294293	0.115498291761	0.0706317649693	-0.181513698191	-0.131468274347	0.223057811436	0.010611649221	-0.384990718554	0.070047688933	0.500644688648	0.0225953688932	-0.0172430706583	0.551722760715	-0.0686066969838	0.37928598112	-14.1864833379	21.5895089534	-42.8561302563
4	0.979234219143	0.453693870694	-0.273358947349	1.70088008007	-0.452553844531	1.66319784051	0.00918755209861	0.178273093435	-0.14274436836	-0.309620569897	-0.125854567242	-0.226114407237	0.14476238651	0.0873838302825	0.0732153082782	0.437931528662	0.0755820016668	0.0287644219334	0.568893572731	-0.051116169885	0.43940990197	3.93383709733	20.7347867859	-42.4154857476
5	3.04948180129	0.229462242756	0.150550206134	2.20578457787	0.317841643756	3.71942774166	0.0221755735839	-0.132413602188	0.0845633620827	-0.0264288283251	0.041446165781	-0.19160360665	-0.272811471251	0.695846991264	-0.0501380455283	0.340911813282	-0.065543101591	-0.0209024245266	0.519407046292	-0.000754231046493	0.338398861217	5.50996908149	54.8237992497	-17.053586016
6	1.59738990473	-0.0718259439646	-0.679831079444	1.30906737013	0.772611516496	2.10064454212	0.0614968431145	0.193605436658	0.149152261686	-0.481241114739	-0.110755713149	-0.196418054153	-0.341570139492	0.416325066954	0.0201223154594	0.616783983599	0.00837576839002	0.0421445311457	0.60324663845	0.146733662537	0.444189506861	4.59650466684	43.9380841647	-47.5696539913
7	2.13650479217	0.012353071441	-1.04256814262	1.23707908489	0.241563660688	1.58155492842	0.000322916468875	0.028760168085	0.0413037477425	-0.231411519267	0.00770270268179	-0.274935075108	0.0411317867274	0.520425803696	-0.0382449225212	0.486082079011	0.0333749114627	0.0312767537332	0.566251686124	0.0537480276333	0.464786215096	6.81880038053	31.2205072455	-43.4094510517
8	1.19108595711	0.369716354564	-0.236132479444	1.58272152353	0.471271881866	1.25888710797	0.0569143004299	0.180916183678	0.0951465772833	-0.267551817856	-0.120117404074	0.288699970981	-0.104610416392	-0.146957625753	0.0476951950204	0.445498719472	0.0699130812415	-0.0857280124703	0.539936950422	0.0493844223783	0.361231767058	-14.1207907073	37.4657635309	-44.4930075943
9	0.520637213837	-0.0990464772844	0.482117438823	3.34675544326	0.0478126617538	1.02620422092	0.0599036541072	0.0688995532663	-0.296794399008	-0.25193510086	0.0840015980216	0.769307502162	0.0889112109015	-0.222621888237	-0.128078338518	0.339742479677	-0.026705513001	-0.0233229400027	0.511403135188	0.0280345162653	0.649892343005	-39.0605942803	49.6055579873	-23.3173379537
10	1.75227673817	-0.658596173421	0.0349276794768	1.49789619628	0.236010242619	1.43449383445	0.0603306286229	0.0443026164688	0.130716209997	-0.198690051626	0.0280989305029	0.295766082603	-0.370557926474	-0.418406878797	0.00451598402786	0.498958776068	0.0656097175802	-0.0137412407279	0.449481801923	0.0526571546467	0.517487117687	-41.3545966394	78.9632515812	-13.4601716293
11	2.38183248565	-0.490577907604	0.594504192486	2.90412620828	0.78993077387	1.81566324392	-0.0196984151478	0.305131687164	0.114920500438	-0.44913789026	0.1379569733	0.0238036095588	-0.320709869557	0.0897530771443	-0.0433296756736	0.447154677149	-0.0335677110741	0.0568887125418	0.330435928123	0.0759577113868	0.339179350372	-24.3827665992	75.5047014386	-21.7299862674
12	2.92863764309	-0.793579442398	0.46043242653	1.62235778568	0.105272867881	2.13954037029	-0.0784788728885	-0.310154229902	0.255565584295	0.198744707139	-0.0194763499001	-0.378825135442	-0.0445036505008	0.367362020167	-0.0552833862078	0.606812848399	-0.0542938174464	-0.0276909015912	0.506878892673	0.025174117702	0.604195855384	-11.5276251805	77.0695728363	0.610691921746
13	3.92886760454	-1.20175567263	1.45010243922	3.67068483862	-1.05114112901	3.23359458788	-0.0948420255407	-0.142597146304	-0.225722442826	0.0409681192035	-0.0218303101011	-0.341959288603	0.0752512474762	0.160728848897	0.0991084705725	0.384934815044	0.0587068799164	0.0266798657644	0.500722798603	0.056468888658	0.600912346318	-15.6167379611	49.1275062276	21.1199288265
14	1.10713446245	0.111247941717	-0.667923881477	3.59560432338	-2.26686422761	2.60571697548	-0.122940292773	-0.286184206387	0.0622167115395	0.538795929538	0.28273856579	-0.0178086168684	-0.373842514825	-0.151532033988	-0.0399469500329	0.590912375428	0.0549901801246	-0.0355688814525	0.558332727209	-0.077707135274	0.510378829249	-23.544253831	67.4365144594	17.1094061874
15	2.03108909876	0.274926466486	0.335975552149	1.83068592358	0.105077266411	1.41371945576	-0.0609639881179	-0.0153973560058	0.23463741463	0.295471217246	0.0336962959365	-0.539458788627	-0.442300082269	0.320635647984	0.0337170286102	0.60503946628	-0.0557316465729	-0.102157196353	0.418182916264	-0.0187359857941	0.601180292471	-14.4938255311	80.3903837043	3.18495531541
16	1.62228207122	0.272696127619	0.24268931851	2.03455254806	-0.980868573886	2.10034663147	0.0515464096941	-0.246413593207	0.259156660544	0.402188333883	-0.0489757571522	-0.0929251895022	-0.657373073659	-0.169349139733	-0.0126137565604	0.608241654714	0.10519375994	0.0156389243378	0.418722251491	-0.0720609931016	0.48261002585	-31.5428167407	79.8387922538	11.9987973372
17	3.07651745474	0.610355096951	0.326394908277	2.10852193806	-0.0862848919584	2.48643376354	0.00496369458238	0.0600815573323	0.296207219952	-0.143375753126	-0.0572324761716	0.382817634631	-0.168802973631	-0.561412833272	-0.0326908027058	0.586176946001	0.149043097461	-0.0139603363826	0.51595098045	0.0815119144767	0.58498806298	-44.3909390337	76.4419462905	-10.1496731844

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 174 )	A	A	1 - 174	1 - 174
2	2	chain 'A' and (resid 175 through 239 )	A	A	175 - 239	175 - 239
3	3	chain 'A' and (resid 240 through 346 )	A	A	240 - 346	240 - 346
4	4	chain 'A' and (resid 347 through 466 )	A	A	347 - 466	347 - 466
5	5	chain 'B' and (resid 1 through 174 )	B	G	1 - 174	1 - 174
6	6	chain 'B' and (resid 175 through 239 )	B	G	175 - 239	175 - 239
7	7	chain 'B' and (resid 240 through 312 )	B	G	240 - 312	240 - 312
8	8	chain 'B' and (resid 313 through 466 )	B	G	313 - 466	313 - 466
9	9	chain 'C' and (resid 2 through 205 )	C	M	2 - 205	1 - 204
10	10	chain 'C' and (resid 206 through 312 )	C	M	206 - 312	205 - 311
11	11	chain 'C' and (resid 313 through 413 )	C	M	313 - 413	312 - 412
12	12	chain 'C' and (resid 414 through 466 )	C	M	414 - 466	413 - 465
13	13	chain 'D' and (resid 1 through 144 )	D	S	1 - 144	1 - 144
14	14	chain 'D' and (resid 145 through 205 )	D	S	145 - 205	145 - 205
15	15	chain 'D' and (resid 206 through 312 )	D	S	206 - 312	206 - 312
16	16	chain 'D' and (resid 313 through 413 )	D	S	313 - 413	313 - 413
17	17	chain 'D' and (resid 414 through 466 )	D	S	414 - 466	414 - 466

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