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- PDB-7cb0: The apo 6-phosphogluconate dehydrogenase from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 7cb0
TitleThe apo 6-phosphogluconate dehydrogenase from Staphylococcus aureus (strain Newman)
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsCYTOSOLIC 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
6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 ...6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsWang, H. / Wang, M. / Sun, H.
Funding support Hong Kong, China, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)1733616P Hong Kong
National Science Foundation (NSF, China)21671203 China
CitationJournal: 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
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase, decarboxylating
B: 6-phosphogluconate dehydrogenase, decarboxylating
C: 6-phosphogluconate dehydrogenase, decarboxylating
D: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)207,4304
Polymers207,4304
Non-polymers00
Water1,56787
1
A: 6-phosphogluconate dehydrogenase, decarboxylating
B: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)103,7152
Polymers103,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-62 kcal/mol
Surface area33020 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase, decarboxylating

D: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)103,7152
Polymers103,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area10360 Å2
ΔGint-66 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.830, 133.050, 165.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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Components

#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 % / Description: Transparent slice chips
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M NaNO3, 0.2M NH4NO3, 22% PEG 3350 (w/v) / PH range: 8.0-8.3 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen Flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2017
RadiationMonochromator: Graphite filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→44.92 Å / Num. obs: 67767 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.073 / Rrim(I) all: 0.265 / Net I/σ(I): 8.3 / Num. measured all: 912466 / Scaling rejects: 284
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.52-2.5913.91.7726928549800.610.4911.841.7100
11.27-44.9211.10.08295458570.9970.0250.08520.998.6

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.18.1refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
MoRDa27phasing
RefinementMethod to determine structure: SAD / Resolution: 2.52→44.91 Å / SU ML: 0.3341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 3507 5.18 %
Rwork0.2023 64171 -
obs0.2047 67678 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.05 Å2
Refinement stepCycle: LAST / Resolution: 2.52→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14394 0 0 87 14481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003114650
X-RAY DIFFRACTIONf_angle_d0.53419788
X-RAY DIFFRACTIONf_chiral_restr0.03882180
X-RAY DIFFRACTIONf_plane_restr0.00332578
X-RAY DIFFRACTIONf_dihedral_angle_d21.2155408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.550.36521450.31682564X-RAY DIFFRACTION99.93
2.55-2.590.33541320.3032537X-RAY DIFFRACTION100
2.59-2.630.39521360.2872536X-RAY DIFFRACTION99.93
2.63-2.670.37621320.29312516X-RAY DIFFRACTION100
2.67-2.710.30571700.27172513X-RAY DIFFRACTION100
2.71-2.760.31131440.27382523X-RAY DIFFRACTION99.96
2.76-2.810.36251570.27952572X-RAY DIFFRACTION99.96
2.81-2.870.32641180.28322525X-RAY DIFFRACTION100
2.87-2.920.33271350.28272528X-RAY DIFFRACTION99.92
2.92-2.990.36321230.25972569X-RAY DIFFRACTION100
2.99-3.060.2981190.23942541X-RAY DIFFRACTION100
3.06-3.130.27251220.22762574X-RAY DIFFRACTION100
3.13-3.220.29871500.23062549X-RAY DIFFRACTION99.96
3.22-3.310.28711430.2322551X-RAY DIFFRACTION100
3.31-3.420.28031430.21472549X-RAY DIFFRACTION100
3.42-3.540.2491410.1922557X-RAY DIFFRACTION100
3.54-3.680.24951320.18422562X-RAY DIFFRACTION99.96
3.68-3.850.20411500.18092566X-RAY DIFFRACTION100
3.85-4.050.24581360.17822576X-RAY DIFFRACTION100
4.05-4.310.18151400.16392579X-RAY DIFFRACTION100
4.31-4.640.2061380.16352578X-RAY DIFFRACTION99.38
4.64-5.110.22431600.17252576X-RAY DIFFRACTION99.96
5.11-5.840.25121480.19182609X-RAY DIFFRACTION100
5.84-7.360.22211510.19292649X-RAY DIFFRACTION100
7.36-44.910.19611420.16612772X-RAY DIFFRACTION99.56
Refinement TLS params.

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

IDL11 (°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)
12.14475570186-0.0950046450019-0.2349273356371.496394302750.0173073127832.18271327372-0.1098893986740.260106483911-0.120767706017-0.195284377318-0.000267840836794-0.250994603820.1415782863920.2379212443150.1209070410050.4128658174140.01117486695030.07466536966470.314247479593-0.01402544450230.3868070051096.6317329152911.9446835411-65.3040585188
20.5789302656620.008926037973330.02477949982231.05790881610.03705738236110.4758101080490.0481859847281-0.04130978932650.001190492636550.0526945003836-0.044724027589-0.00539210623380.0937243736938-0.0280914653046-0.00110414708250.334610086038-0.00866185853330.02461569240860.2926698258850.02539109355170.321933643073-5.17466364630.6579558532-39.5008206113
31.93374235756-0.1825365220820.5869736029022.167077998830.1518050067342.895109410240.02588005448890.1697044892560.0220943004804-0.178112838995-0.05488543576080.397127039650.0315616903523-0.2405203134470.01493817370490.33930426843-0.000116987139447-0.05517373267350.3270043486680.02476894290840.389547216745-15.642504539561.6110910323-72.1517949151
40.5691918694710.03233296209790.07918709373011.21883920739-0.144348205890.7652536740820.0134594798465-0.08505972489760.0336358022650.0284984585952-0.009997196792510.0879089781855-0.0544205264166-0.042244298655-0.003633343468740.3087565599740.01613418163950.003547755072790.251128402483-0.008033060101430.294816148437-8.1780089651349.1617371641-41.5446385546
52.2050933216-0.318662167923-0.6638779738452.14290651839-0.4451475050672.341151678560.0117495512285-0.02045605182650.2238201181730.07702537072310.02899361487890.662242036105-0.0649267968879-0.5005128361010.002276078922310.4484964162790.0226888928904-0.0340153866520.618937813831-0.006397045192470.642109940991-38.88066298120.4158435931-58.3920094628
60.5077176631520.0101376606212-0.404034495491.21650560484-0.02118457581341.16742969146-0.04486203093890.0155932622136-0.108507982840.07368578807540.1032902957630.001614512258230.113349614966-0.0768245252776-0.07173114037450.367219638874-0.0426871339673-0.01184971832050.4405613783070.008387979636570.377722798363-27.5724479335-9.70982435948-67.3540860378
71.76536741822-0.9038982474720.7573468317432.60964227944-0.06708217926742.37384383121-0.0188737012040.244229892737-0.427136593899-0.2377761011590.1321490193560.5969054643580.01107939931750.0799973651564-0.09503125453860.465961521198-0.0958976762892-0.02260323089410.7158023434220.004401926371740.632609364948-28.6062527252-10.1324144768-25.4020470282
81.48698367157-0.523881679882-0.4478848580882.352561318841.53184570681.83879417986-0.09670357688690.1825393915730.17651699737-0.7287424905890.09070504853080.418199044568-0.7726432497870.05124819503840.04761790791430.712226554194-0.120067196929-0.1032971275460.5047567856520.167703582840.575648503423-28.815125813516.7177310922-9.50078052444
94.32896103112-0.09811060398980.03766908387791.56131290190.1506148278122.81452322453-0.1292664148690.2861029334490.443410134421-0.4185008247960.1816152861240.34543960301-0.112113300165-0.247073554811-0.01940701388420.497907965867-0.116200197805-0.05575501790090.478171928770.09057539104890.563313778589-29.77605035857.76616773807-1.68510232308
102.29531803569-0.9590701089020.1790143947492.20339518166-0.1056089488535.851814600320.1826763374410.04717175047820.1852316900570.378435362549-0.01687777728910.213935553667-0.605590535363-0.0203188583318-0.2955867143710.386116805441-0.001975450723620.05118200177890.5588266463740.0686971663970.490805815898-34.72703387118.994075226912.3623772494
110.538858159211-0.258533554045-0.2257207768762.377285440140.4862734097331.31396381754-0.1071728897770.3340165201450.175086385213-0.3303862968310.0827387740137-0.208711202444-0.1371550737920.2195848642570.02530159546910.659361284645-0.2335688261970.01035319314810.8142309831390.1056675593310.510425600281-13.954940134411.8802728507-13.1123953266
121.62685871399-0.4635939862640.388570094531.31796899911-0.104197445371.2443939558-0.1759233438220.1903247451230.382217008409-0.08589597821130.0850605065732-0.390153553665-0.2235119266880.3316190810910.1091216664810.569143106985-0.1783646154660.002578482881080.703134865344-0.02139418778880.572694109914-6.4957805456414.77721823517.02137516729
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 466 )AA175 - 466175 - 466
33chain 'B' and (resid 1 through 174 )BB1 - 1741 - 174
44chain 'B' and (resid 175 through 466 )BB175 - 466175 - 466
55chain 'C' and (resid 1 through 174 )CC1 - 1741 - 174
66chain 'C' and (resid 175 through 466 )CC175 - 466175 - 466
77chain 'D' and (resid 2 through 174 )DD2 - 1741 - 173
88chain 'D' and (resid 175 through 239 )DD175 - 239174 - 238
99chain 'D' and (resid 240 through 290 )DD240 - 290239 - 289
1010chain 'D' and (resid 291 through 312 )DD291 - 312290 - 311
1111chain 'D' and (resid 313 through 389 )DD313 - 389312 - 388
1212chain 'D' and (resid 390 through 465 )DD390 - 465389 - 464

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