PDB-7cb2: The 6-phosphogluconate dehydrogenase (NADP-bound) from Staphyloco...

ID or keywords:

Entry

Database: PDB / ID: 7cb2

Title

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

Components

6-phosphogluconate dehydrogenase, decarboxylating

Keywords

CYTOSOLIC PROTEIN / Pentose phosphate pathway / decarboxylating

Function / homology

Function and homology information

phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / organic acid catabolic process / pentose-phosphate shunt / NADP binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

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

Funding support

Hong Kong,

China, 2items

Citation

Journal: To Be Published
Title: The 6-phosphogluconate dehydrogenase (NADP-bound) structures from Staphylococcus aureus
Authors: Wang, H. / Wang, M. / Sun, H.

History

Deposition	Jun 10, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 16, 2021	Provider: repository / Type: Initial release
Revision 1.1	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	7cb2.cif.gz	811.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7cb2.ent.gz	600.4 KB	Display	PDB format
PDBx/mmJSON format	7cb2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7cb2_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7cb2_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7cb2_validation.xml.gz	64.1 KB	Display
Data in CIF	7cb2_validation.cif.gz	86.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/7cb2 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cb2	HTTPS FTP

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Related structure data

Related structure data	7cb0S S: Starting model for refinement
Similar structure data	2jkv-3 2iz1-2 7cb0-1 5uq9-2 2iyp-2 7cb0-2 2iyp-1 4gwg-2 2zyg-2 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

211 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
106 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.530, 136.040, 164.540
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.58 Å³/Da / Density % sol: 52.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M NaNO3, 0.2M NH4NO3, 0.1M MES, 22% PEG3350 (w/v) 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: 0.97917 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97917 Å / Relative weight: 1

Reflection

Resolution: 2.15→47.76 Å / Num. obs: 116921 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.142 / R_pim(I) all: 0.041 / R_rim(I) all: 0.148 / Net I/σ(I): 12 / Num. measured all: 1532159 / Scaling rejects: 946

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
2.15-2.21	13.7	1.384	117228	8564	0.81	0.387	1.438	2.4	100
9.62-47.76	10.8	0.06	15738	1453	0.998	0.018	0.063	27.9	98.7

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Processing

Software

Name	Version	Classification
Aimless	0.6.2	data scaling
PHENIX	1.18.1	refinement
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
PHASER	2.8.1	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7CB0

7cb0

Resolution: 2.15→47.76 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2225	5958	5.11 %
R_work	0.1975	110740	-
obs	0.1987	116698	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: 55.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→47.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14405	0	176	196	14777

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	14841
X-RAY DIFFRACTION	f_angle_d	0.5544	20075
X-RAY DIFFRACTION	f_chiral_restr	0.0389	2205
X-RAY DIFFRACTION	f_plane_restr	0.0027	2589
X-RAY DIFFRACTION	f_dihedral_angle_d	21.9386	5481

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 (%)
2.15-2.17	0.3253	225	0.2893	3636	X-RAY DIFFRACTION	99.9
2.17-2.2	0.3006	195	0.2773	3638	X-RAY DIFFRACTION	99.95
2.2-2.23	0.3146	190	0.2686	3675	X-RAY DIFFRACTION	99.9
2.23-2.26	0.3061	197	0.2745	3663	X-RAY DIFFRACTION	99.87
2.26-2.28	0.297	193	0.2809	3649	X-RAY DIFFRACTION	99.84
2.28-2.32	0.2961	213	0.2647	3659	X-RAY DIFFRACTION	99.87
2.32-2.35	0.3058	179	0.2631	3674	X-RAY DIFFRACTION	99.84
2.35-2.38	0.2863	186	0.2613	3656	X-RAY DIFFRACTION	99.84
2.38-2.42	0.3086	195	0.2574	3643	X-RAY DIFFRACTION	99.58
2.42-2.46	0.2715	203	0.2621	3649	X-RAY DIFFRACTION	99.69
2.46-2.5	0.3324	185	0.2664	3646	X-RAY DIFFRACTION	99.38
2.5-2.55	0.3236	192	0.2615	3657	X-RAY DIFFRACTION	99.61
2.55-2.6	0.2639	199	0.2481	3696	X-RAY DIFFRACTION	99.8
2.6-2.65	0.2862	196	0.2391	3676	X-RAY DIFFRACTION	99.82
2.65-2.71	0.2645	217	0.2424	3616	X-RAY DIFFRACTION	99.9
2.71-2.77	0.2463	187	0.2498	3708	X-RAY DIFFRACTION	99.92
2.77-2.84	0.2842	219	0.2416	3649	X-RAY DIFFRACTION	99.82
2.84-2.92	0.2683	183	0.2433	3691	X-RAY DIFFRACTION	99.9
2.92-3	0.2496	212	0.2297	3678	X-RAY DIFFRACTION	99.79
3-3.1	0.2473	196	0.2261	3680	X-RAY DIFFRACTION	99.77
3.1-3.21	0.2458	206	0.227	3681	X-RAY DIFFRACTION	99.92
3.21-3.34	0.2257	195	0.2183	3705	X-RAY DIFFRACTION	99.77
3.34-3.49	0.2293	197	0.2031	3701	X-RAY DIFFRACTION	99.9
3.49-3.68	0.2122	180	0.1867	3747	X-RAY DIFFRACTION	99.87
3.68-3.91	0.2056	185	0.1745	3702	X-RAY DIFFRACTION	99.72
3.91-4.21	0.1745	225	0.161	3712	X-RAY DIFFRACTION	99.82
4.21-4.63	0.1571	185	0.1482	3742	X-RAY DIFFRACTION	99.64
4.63-5.3	0.1895	187	0.1583	3787	X-RAY DIFFRACTION	99.75
5.3-6.67	0.1893	205	0.1825	3803	X-RAY DIFFRACTION	99.95
6.68-47.76	0.1747	231	0.1393	3921	X-RAY DIFFRACTION	99.14

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	3.57972212972	0.766992875299	-0.482057187437	2.37871031079	0.302032756418	4.04939011934	0.0273390618212	-0.396505446938	0.00663342970261	0.102898565279	-0.15690084528	0.192205614125	0.118509396452	-0.321298251318	0.131870075779	0.286017240812	0.00103512919593	0.0317246410114	0.268382699065	0.00407614179511	0.277214458316	-7.89635007785	-57.2743871782	-15.6721159986
2	2.76539464442	-1.04698295049	3.53055562283	2.26703043695	-1.94860900971	7.41937870817	0.0031760451368	0.220283552673	-0.0392571839758	-0.505528152617	-0.0210587546981	0.305066864259	-0.0504519272492	-0.210258767347	0.0979166491736	0.383415279547	0.0300734999446	-0.0201909792481	0.277605339383	-0.0252975617928	0.336790000334	-8.15018875907	-45.7097809445	-45.0748654175
3	8.36521726881	2.48492704034	5.16147152445	3.25063447194	1.45273594673	4.78514582283	0.246836181844	-0.343775054634	-0.0709462803297	-0.107519849962	-0.150171495319	0.5000614853	0.110660410928	-0.595998459187	-0.0518899578499	0.323631304516	0.0200156152391	0.0205011906339	0.299702857653	0.0291165306576	0.349594319655	-8.84613776898	-36.5931857254	-37.3030701941
4	0.518241750161	0.0189624643534	0.100608344718	1.80532287921	-0.273875414501	0.794932729529	0.0320761044264	0.0264387093958	-0.0457049920791	-0.325097762669	-0.0499112606876	-0.166573913423	0.0865627965632	-0.0246774401718	0.0199388001913	0.390855589811	0.056542402059	0.0552280552263	0.296457546977	-0.00984078683923	0.325602480744	8.31892548412	-38.4132290542	-43.5943784712
5	4.59901942207	0.904735341238	0.854322856095	2.87710938704	-0.471314167563	4.68963069264	-0.0985192903165	-0.541992332906	0.0304729422574	0.0345179957704	-0.143658991304	-0.226741102991	-0.186669152044	0.373593373103	0.246851659222	0.31882601507	0.0627185481879	-0.030145131909	0.352286856869	-0.0166638345841	0.293136664171	15.3126779035	-7.32626547769	-12.1743705973
6	0.568804313634	0.132462035657	0.0532266503554	1.89952237384	0.0966267179314	0.929248579789	0.0360746386836	0.0600258525726	0.0644719838089	-0.26664630377	-0.0338230661714	-0.183409330553	-0.152225605329	0.0460545363579	0.00482381814173	0.415998341019	0.0570933707083	0.0298644579875	0.289736820801	0.0241122912035	0.345324714714	4.93707593455	-21.1404039046	-41.539732121
7	3.79187761922	0.308606278033	0.473321569112	3.25818924988	0.360971654259	2.67803482263	-0.134112374718	0.420982445732	-0.410899060606	-0.42685835574	0.226776125649	0.605470653705	0.645463951903	-0.685762632688	-0.0645016159275	0.574891662196	-0.222073291276	-0.051832837377	0.595690555805	0.00860843856632	0.507391135567	-29.3094126452	-13.5427967793	-25.1917802633
8	8.20653112328	-5.54548653316	-5.43840681462	4.02158257409	4.4237590877	5.58940233332	0.151178213709	0.11211505653	0.53954402962	-0.107274721449	0.226445614956	-0.141319763474	-0.287705817845	-0.144065455425	-0.20699964365	0.332837950478	-0.000751022498976	-0.0112269825216	0.298175455782	0.0910915847933	0.294980334587	-26.1941232835	8.06155052341	-9.27137418779
9	2.31770221044	0.187157845096	-0.401234287692	1.52732079729	-0.41004774449	2.01861240603	0.165492070919	0.231212023348	0.481825870325	-0.112613288946	0.105392551755	0.490012419749	-0.376355010849	-0.491565257859	-0.202957439041	0.385977148234	0.0621435253497	0.0349702801907	0.374913877823	0.0754519694432	0.501026720948	-32.8590313094	14.2912469221	-5.45594767204
10	1.85758952053	-1.23371109433	-0.589892853092	5.94333881587	1.30314122527	2.42586329654	0.111141963389	0.128441827593	0.274542964707	-0.458831657748	0.0541916726301	-0.00894539210577	-0.356148930807	0.144973924303	-0.144119626228	0.415653343799	-0.0304341526667	0.0668754856653	0.298052105181	0.0643381906935	0.319174667887	-14.6605586544	9.74151977977	-14.9295276734
11	0.629903744454	-0.293224710078	0.00525139403108	1.37607439879	-0.790977262984	3.25437790139	0.0937546811103	-0.0636694723049	0.203377312132	0.0972747217476	-0.0863424636212	-0.176149225675	-0.317348329227	0.499027801118	0.0267941042799	0.435381226367	-0.131073442705	0.069136884383	0.404285602812	-0.035795651083	0.485250575304	-7.99209851184	13.9044031896	5.70105527035
12	3.31463344646	-1.03055040055	0.507384171094	3.9789796794	0.923012180549	4.03939419418	-0.0944707301851	-0.277450023781	-0.476465917829	0.273898990981	0.124440879789	-0.346564613392	0.384581595203	0.759489384495	-0.0363140348681	0.36580928834	0.0624621657022	0.00998098672103	0.515714787067	0.162107938089	0.510666067065	-10.5465917734	-19.1713778015	26.2392316159
13	1.16459370175	0.251972903784	-0.2483143727	1.26019980921	-0.321300846774	1.78914729138	0.144315580193	-0.180837091947	0.18026468916	0.26770376256	-0.0294415325632	0.00596760384883	-0.295412780901	0.108037773514	-0.0958128282487	0.364659192203	-0.0347914154613	0.0649709515933	0.272818790595	-0.0379242305777	0.345976274923	-20.098527541	10.0177162332	13.410698425

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 290 )	A	A	240 - 290	240 - 290
4	4	chain 'A' and (resid 291 through 466 )	A	A	291 - 466	291 - 466
5	5	chain 'B' and (resid 1 through 174 )	B	B	1 - 174	1 - 174
6	6	chain 'B' and (resid 175 through 466 )	B	B	175 - 466	175 - 466
7	7	chain 'C' and (resid 1 through 174 )	C	C	1 - 174	1 - 174
8	8	chain 'C' and (resid 175 through 205 )	C	C	175 - 205	175 - 205
9	9	chain 'C' and (resid 206 through 312 )	C	C	206 - 312	206 - 312
10	10	chain 'C' and (resid 313 through 389 )	C	C	313 - 389	313 - 389
11	11	chain 'C' and (resid 390 through 466 )	C	C	390 - 466	390 - 466
12	12	chain 'D' and (resid 1 through 174 )	D	D	1 - 174	1 - 174
13	13	chain 'D' and (resid 175 through 466 )	D	D	175 - 466	175 - 466

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