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- PDB-8d5h: Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from... -

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Entry
Database: PDB / ID: 8d5h
TitleCrystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin
ComponentsfolP-SMZ_B27
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / DIHYDROPTEROATE SYNTHASE / HYDROLASE / OXIDOREDUCTASE
Function / homology6-HYDROXYMETHYLPTERIN / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsStogios, P.J. / Skarina, T. / Osipiuk, J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin
Authors: Stogios, P.J.
History
DepositionJun 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: folP-SMZ_B27
B: folP-SMZ_B27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61614
Polymers59,2792
Non-polymers1,33712
Water12,809711
1
A: folP-SMZ_B27
hetero molecules

A: folP-SMZ_B27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,73716
Polymers59,2792
Non-polymers1,45814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area5890 Å2
ΔGint-91 kcal/mol
Surface area21900 Å2
MethodPISA
2
B: folP-SMZ_B27
hetero molecules

B: folP-SMZ_B27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,49512
Polymers59,2792
Non-polymers1,21510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4770 Å2
ΔGint-39 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.781, 101.781, 207.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-306-

SO4

21A-760-

HOH

31B-421-

HOH

41B-727-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein folP-SMZ_B27


Mass: 29639.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: folP-SMZ_B27 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold

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Non-polymers , 5 types, 723 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% (w/v) PEG 5K MME, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6, 1 mM 6-hydroxymethyl-7,8-dihydropterin pyrophosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.72→25 Å / Num. obs: 68078 / % possible obs: 100 % / Redundancy: 30.5 % / Biso Wilson estimate: 22.76 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.021 / Net I/σ(I): 28
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 27.8 % / Rmerge(I) obs: 1.398 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3352 / CC1/2: 0.81 / Rpim(I) all: 0.267 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VIS

5vis


Resolution: 1.72→24.85 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1832 1951 2.95 %
Rwork0.1537 64245 -
obs0.1545 66196 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.2 Å2
Refinement stepCycle: LAST / Resolution: 1.72→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 81 711 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01374269
X-RAY DIFFRACTIONf_angle_d1.19665781
X-RAY DIFFRACTIONf_chiral_restr0.0839668
X-RAY DIFFRACTIONf_plane_restr0.0117751
X-RAY DIFFRACTIONf_dihedral_angle_d14.07521579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.30681280.27424178X-RAY DIFFRACTION90.23
1.76-1.810.24961290.22834309X-RAY DIFFRACTION93.24
1.81-1.860.20671340.18554372X-RAY DIFFRACTION94.43
1.86-1.920.20161360.16234469X-RAY DIFFRACTION95.92
1.92-1.990.20161350.16094492X-RAY DIFFRACTION96.82
1.99-2.070.20781410.16184543X-RAY DIFFRACTION97.69
2.07-2.170.17191390.15634584X-RAY DIFFRACTION98.29
2.17-2.280.18011380.14694616X-RAY DIFFRACTION98.86
2.28-2.420.19181410.14844656X-RAY DIFFRACTION98.89
2.42-2.610.20741420.15244650X-RAY DIFFRACTION99.05
2.61-2.870.19311440.15394700X-RAY DIFFRACTION99.4
2.87-3.290.19321420.15014774X-RAY DIFFRACTION99.61
3.29-4.140.14131470.12674813X-RAY DIFFRACTION99.78
4.14-24.850.16941550.15645089X-RAY DIFFRACTION99.41
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)
16.072866707525.46685866991-3.44449597728.67690199769-3.896282241055.264797486340.0839731680589-0.36881121418-0.3345664900630.0884639069907-0.05564987627850.01044028777720.567005365316-0.1670891884510.04887527577390.243105000797-0.00739182953352-0.004172776437910.2222908570080.02693917412670.191261140917-6.6303115644822.207894212817.3477015037
27.380537316394.25926793953-5.441916308392.98065226564-3.5165806734.72100958416-0.8236908947420.0882956376831-0.7310967434150.2374770553320.1509515989170.5377349959191.6023060841-0.458516417490.466621608190.685204863669-0.006707834192610.190409824630.2878672075460.01879154564290.395772088652-6.0521208678710.854626846620.7784105638
31.14014166928-0.4786356677120.4309780811111.35510250201-0.9775009417932.02990685228-0.0508693930835-0.177344894377-0.04671573486460.2001341547540.0608461337160.061215392605-0.00927638569763-0.115392708529-0.01095016518610.1415630737510.004664995252790.01996972567680.13462234312-0.01458356043980.118083892647-16.402639437331.286877770518.0431391691
41.702803794050.30354778814-0.7153101553272.585564827370.9156441370333.1779980527-0.1489303310060.0502359866822-0.0774256655786-0.03608565646990.02998070019440.01286527890710.235999945417-0.03320005962030.1138636365530.1198711315030.003915328237310.0160544884810.1001743703790.01703152839370.0857129775743-4.1739170521527.56883142385.59402302391
50.655031242111-0.886385711724-1.508618734291.215988125512.086174719463.6288136373-0.992214613562-0.7150271971790.8678048604313.861186213961.11999651113-2.540824497120.951390424971.34870384044-0.1202405611581.204090642720.139627717041-0.3897096932021.27840729331-0.3144824191250.70397053447119.703802442641.06189133298.11725793089
63.427403311013.97022153874-1.420701806576.72611215801-1.44731736233.84120488375-0.04724030844180.06913995342020.28417639831-0.1219358163680.0924800363356-0.448733457794-0.4484400126070.6066777541410.04158220122330.313359613769-0.106082173201-0.01831094760490.317203793634-0.02948249652930.371878512453-21.269656848410.7392489835-17.1875075955
77.937087962525.00436652182-5.0523551463.68627545371-4.68922898569.095241097530.01217186392760.03750347060940.605437169064-0.0609698602751-0.569910854676-0.975452927624-0.7157635896211.284700311830.4866179088290.32717530207-0.07122262091680.01004276887450.5032790080820.1383550027240.499222409555-12.56312253048.00603928778-21.0378364007
81.68259863882-1.00622591153-0.06696209383920.6149162572380.2059982943251.933039748310.143000813144-0.3193718681690.4004885565170.240289153634-0.0316763636744-0.293559826597-0.4347900231380.273792494515-0.09644445337540.320164592614-0.1219573646620.03145687654170.26948921356-0.06368037820950.231739852187-23.060294845217.6633032029-16.7303117812
92.5899338453-2.07266872504-0.6946401711393.296789498991.491271175151.636083799720.2745356459430.3405976278870.210584489161-0.587033064209-0.154432321664-0.222046325073-0.3635380124140.0619842526297-0.1056323215880.386908626418-0.06218411679370.0327376274630.2979838003560.037267728340.160182036102-22.559501090415.4662250153-27.7893504526
102.05836172033-0.198316568406-0.7447171593541.118307410270.1824824394573.446567719530.005061636425840.2885127573870.161402910126-0.392720812319-0.04344957972510.171356324581-0.317303858477-0.08635143406460.03953895271860.2519840247440.000606690357272-0.0721880174390.1480424378530.02080330449250.173673176172-34.979765248121.0150681849-16.2971901656
112.13957639125-0.00351130445410.4938902559091.30821719851-0.03952955782174.50774401181-0.0804348599420.207623881267-0.0048283213734-0.219841123774-0.04574955242880.3253092751350.00774351118569-0.3802107371420.1049489721910.1433851300610.00470385605305-0.05185518917280.164448515437-0.01616238661250.208357886577-41.651425063815.4905012043-10.415240148
124.09901644760.0418679254541.857343240261.89119108908-0.2635491323413.0943296915-0.08074099101540.01932964526210.02940151677530.01830260816670.01082624175530.0321315875984-0.055556359434-0.04985333273540.08717315878010.150988201261-0.002404398981760.001375690326490.0798588079714-0.01049790959110.117866989959-29.10663722138.17570076937-4.3615006275
137.150212398282.36502082567-1.489613671914.00383589084-1.731660248474.67119615239-0.1855969134450.328215556668-0.603067758181-0.22641808580.1907954797570.09561143535510.369273291501-0.281949735231-0.09041823111270.211432781786-0.0156010699598-0.008611257406380.113898761069-0.03338908905020.166839113535-32.9941972525-7.24718526326-8.10624293661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 22 )AA0 - 221 - 17
22chain 'A' and (resid 23 through 39 )AA23 - 3918 - 34
33chain 'A' and (resid 40 through 204 )AA40 - 20435 - 199
44chain 'A' and (resid 205 through 270 )AA205 - 270200 - 265
55chain 'A' and (resid 271 through 271 )AA271266
66chain 'B' and (resid -1 through 21 )BD-1 - 211 - 23
77chain 'B' and (resid 22 through 39 )BD22 - 3924 - 41
88chain 'B' and (resid 40 through 59 )BD40 - 5942 - 61
99chain 'B' and (resid 60 through 99 )BD60 - 9962 - 101
1010chain 'B' and (resid 100 through 148 )BD100 - 148102 - 150
1111chain 'B' and (resid 149 through 204 )BD149 - 204151 - 206
1212chain 'B' and (resid 205 through 252 )BD205 - 252207 - 254
1313chain 'B' and (resid 253 through 272 )BD253 - 272255 - 274

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