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- PDB-9f7o: N-acetylglucosamine 6-phosphate dehydratase: apo form of NagS -

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Basic information

Entry
Database: PDB / ID: 9f7o
TitleN-acetylglucosamine 6-phosphate dehydratase: apo form of NagS
ComponentsUPF0309 protein SCO4393
KeywordsSUGAR BINDING PROTEIN / Central metabolism / Aminosugar dehydratase / GlcNac-6P / Aminosugar toxicity
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
Uncharacterised protein family UPF0309 / RpiR-like, SIS domain / : / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily
Similarity search - Domain/homology
UPF0309 protein SCO4393
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbrahams, J.P. / Li, C.
Funding support China, Netherlands, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council201904910552 China
Netherlands Organisation for Scientific Research (NWO)10379 Netherlands
Citation
Journal: Biorxiv / Year: 2024
Title: A new pathway in central metabolism mediates nutrient control of development and antibiotic production by Streptomyces
Authors: Li, C. / Urem, M. / Kotsogianni, I. / Lau, J. / Elsayed, S.S. / Martin, N.I. / McNae, I.W. / Voskamp, P. / Mayer, C. / Rigali, S. / Pannu, N. / Abrahams, J.P. / Schada von Borzyskowski, L. / van Wezel, G.P.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0309 protein SCO4393
B: UPF0309 protein SCO4393
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6866
Polymers52,3012
Non-polymers3844
Water4,378243
1
A: UPF0309 protein SCO4393
hetero molecules

A: UPF0309 protein SCO4393
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6866
Polymers52,3012
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area6610 Å2
ΔGint-106 kcal/mol
Surface area17820 Å2
MethodPISA
2
B: UPF0309 protein SCO4393
hetero molecules

B: UPF0309 protein SCO4393
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6866
Polymers52,3012
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_754-x+y+2,y,-z-1/21
Buried area6640 Å2
ΔGint-102 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.694, 87.694, 273.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-486-

HOH

31B-478-

HOH

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Components

#1: Protein UPF0309 protein SCO4393


Mass: 26150.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO4393, SCD10.25c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K3V1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulphate, 0.1 M BIS-Tris, pH 5.5; after crystallosation, crystals were soaked in mother liquor with 10-20% glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→44.4 Å / Num. obs: 147833 / % possible obs: 97.53 % / Redundancy: 5.3 % / Biso Wilson estimate: 30.04 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2646 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.38 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1380 4.95 %
Rwork0.1806 26513 -
obs0.1822 27893 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 20 243 3887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853694
X-RAY DIFFRACTIONf_angle_d0.90565032
X-RAY DIFFRACTIONf_chiral_restr0.0526606
X-RAY DIFFRACTIONf_plane_restr0.0085658
X-RAY DIFFRACTIONf_dihedral_angle_d11.70581308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.30571240.2542522X-RAY DIFFRACTION96.01
2.38-2.480.28761130.22252652X-RAY DIFFRACTION98.93
2.48-2.590.24441340.18952614X-RAY DIFFRACTION98.57
2.59-2.730.21111460.18282632X-RAY DIFFRACTION98.69
2.73-2.90.23451320.18822642X-RAY DIFFRACTION98.51
2.9-3.120.23151450.1932628X-RAY DIFFRACTION98.16
3.12-3.440.21431500.17992629X-RAY DIFFRACTION97.82
3.44-3.940.1841320.15782673X-RAY DIFFRACTION97.46
3.94-4.960.1911520.14642678X-RAY DIFFRACTION96.65
4.96-44.380.19991520.18972843X-RAY DIFFRACTION95.14
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)
10.03546487050520.09205367466640.03892395060810.1404224835180.05825959531880.0770953104197-0.02537509881960.0482644372270.109149621415-0.0695744038132-0.137944292862-0.328908492778-0.1961385729230.6779487829520.0005599564992070.241082499797-0.03715271339250.003023462911130.401085621136-0.03460734132450.32708039490478.537699468539.0626392644-23.3259181513
20.3475319476140.1460081423920.002174011748970.2421673332260.3411920003750.5523916154440.01896998240670.0443200104121-0.00735187246049-0.1109939766170.01623525508960.0538251410654-0.0604807084576-0.05970615185131.48070246961E-80.229546441089-0.01230057729540.005534185176580.2563889492280.01654239621360.24094799051755.7446844434.5221580286-33.6654149263
30.02628483381170.04272916914210.02410691347650.05191051160810.05922043061390.0660131538374-0.0769355117925-0.05369241758940.103191021366-0.2255033148390.193522647188-0.06572833189960.176755944992-0.142533459523-1.54155942488E-70.258595901606-0.0384993623751-0.008955494629090.2918898674130.006033993703640.29919201190457.101979287232.379639628-39.5933876912
40.180071812744-0.119501067597-0.1055941522410.0356387232250.003597709638890.160672423035-0.1044849852770.3966871103690.00983179593054-0.194747587610.0737879955382-0.00316231146193-0.04576392412670.06143417591787.56200846789E-80.269338403902-0.05416126781740.02212002994110.2798904726250.005519686720210.248597441962.158838455629.844432699-42.2558841578
51.035230017170.05372748261780.09700226398840.1729878864320.13485347390.68563280098-0.0442070890807-0.04717736320440.0343384143785-0.05203498736610.0656428368043-0.06458844229530.005932462721780.1528633248175.32050885891E-80.250509804604-0.01909991396420.02193706768950.2706471966460.002953455568780.23596868828365.850639688937.3538502817-31.8644759112
61.09220109610.463678102018-0.786505599680.81261846632-0.2408976833590.587303201549-0.1276389053990.4343437115960.549474179782-0.1459766152910.2080056867610.30882475244-0.409760710583-0.5883182569620.1407964901490.4271346913270.121652208685-0.02871782271510.4167424434530.04320065056060.48824888592643.39325722349.4663376777-31.228686628
70.087022222153-0.06113875830220.0003794143926530.09422012500960.08684887725240.2034865041630.0607290528561-0.413165402558-0.3864333624660.1747806684440.0542640629127-0.05917559571030.292873239887-0.1177861038520.001207427088840.439220463606-0.0133472952409-0.03073754404840.2253834247950.006887951265740.31514204687988.960461439418.4373745016-62.9667446857
80.03414677465260.01419020999260.04907443432760.0292143739173-0.01648722380430.0233499555698-0.1062516704730.112024731642-0.1420071481610.3224842561690.06654179115910.3000343002740.0585858106048-0.000333934475838-0.000711903355220.286585514945-0.0692355185353-0.01777297456060.30960003667-0.007460016841650.26204803293766.841927314228.1734966316-71.2377183184
90.00652828908386-0.0501177878604-0.06972848142380.207567331470.35165657390.3695140778180.0188714163959-0.03255006392580.041105364705-0.00353011227802-0.002329311926130.00386266811348-0.0289373668206-0.03080383918115.87636620936E-80.247639336621-0.002546139052910.008841691505410.218354111708-0.002758656773170.24473503936379.327181568343.7233690201-65.6826271726
100.257378848229-0.104650852542-0.209295556870.03400157964270.04651623386560.1236640184510.0919487194817-0.01354062574950.1804740972140.131009883631-0.2015506683170.00633576474570.1292481228450.274651005234-7.05920534094E-70.214693914414-0.0378804646266-0.00804933708880.269793833398-0.01424284280130.26368429007771.988358157240.342366781-62.5387505595
110.0780451336024-0.08059340597260.01071482691130.06379425247140.03546270228290.051528024457-0.251147218292-0.3285456894680.03199060736390.2722333618110.00850628228224-0.2573330479770.0837634887004-0.0162216795138-0.0004452028629150.272795273445-0.0142230030130.04977301851960.3047361509260.004066652059890.26967657307168.770742654443.1567676352-57.2722623324
120.1365872109620.0496958603276-0.04472392531490.152181410004-0.02037022767520.01542648583280.100961113088-0.2448992158450.09450312936020.0211947157879-0.195209488827-0.1455794818580.435803276009-0.133055155852-1.94152498331E-60.322724463944-0.0550600022435-0.01898939933710.294665457460.007313864164610.25940010157773.082018768331.8081613794-56.9290842319
130.38956314468-0.0564945833317-0.04359067691460.2451046643640.1729881238070.1030951412980.0468829988524-0.0344242018746-0.09226637468190.0217439965447-0.0272017019958-0.02800859830320.2038753769070.0327904553575-1.13608528826E-80.242007729547-0.0291023160616-0.01090622636110.2386102273110.008917164681640.21513721978379.356509889930.3031455874-64.8983190724
140.0825330949122-0.044477810481-0.118602255270.02317389364630.05873075017360.1118446394780.1237500092850.1435567952370.15093915654-0.251041311211-0.0737399469562-0.213407224536-0.2667534560010.0507965462016-1.75510449736E-70.349935647851-0.0266406847701-0.0264120338140.3661959852610.02902180314610.31312956179372.840456779643.6310137248-85.7499511212
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 24 )AA4 - 241 - 21
22chain 'A' and (resid 25 through 106 )AA25 - 10622 - 103
33chain 'A' and (resid 107 through 124 )AA107 - 124104 - 121
44chain 'A' and (resid 125 through 152 )AA125 - 152122 - 149
55chain 'A' and (resid 153 through 231 )AA153 - 231150 - 228
66chain 'A' and (resid 232 through 251 )AA232 - 251229 - 248
77chain 'B' and (resid 4 through 24 )BD4 - 241 - 21
88chain 'B' and (resid 25 through 41 )BD25 - 4122 - 38
99chain 'B' and (resid 42 through 106 )BD42 - 10639 - 103
1010chain 'B' and (resid 107 through 124 )BD107 - 124104 - 121
1111chain 'B' and (resid 125 through 137 )BD125 - 137122 - 134
1212chain 'B' and (resid 138 through 152 )BD138 - 152135 - 149
1313chain 'B' and (resid 153 through 231 )BD153 - 231150 - 228
1414chain 'B' and (resid 232 through 251 )BD232 - 251229 - 248

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