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- PDB-8d5i: Crystal structure of dihydropteroate synthase H182G mutant (folP-... -

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Basic information

Entry
Database: PDB / ID: 8d5i
TitleCrystal structure of dihydropteroate synthase H182G mutant (folP-SMZ_B27) from soil uncultured bacterium in complex with pteroic acid and pyrophosphate
ComponentsfolP-SMZ_B27
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / DIHYDROPTEROATE SYNTHASE / HYDROLASE / OXIDOREDUCTASE
Function / homologyPYROPHOSPHATE 2- / PTEROIC ACID
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsStogios, P.J. / Skarina, T. / Kim, Y. / Di Leo, R. / Venkatesan, M. / 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 H182G mutant (folP-SMZ_B27) from soil uncultured bacterium in complex with pteroic acid
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,5475
Polymers58,7472
Non-polymers8013
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.167, 145.614, 36.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-456-

HOH

21B-700-

HOH

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Components

#1: Protein folP-SMZ_B27


Mass: 29373.408 Da / Num. of mol.: 2 / Mutation: H182G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
#2: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 1% DMSO, 0.1 M Hepes pH 7.5, 5 mM para-aminobenzoic acid, 1.2 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: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 42814 / % possible obs: 98.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.075 / Net I/σ(I): 16.5
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1703 / CC1/2: 0.982 / Rpim(I) all: 0.583 / % possible all: 79.5

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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: 1.82→42.41 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1995 4.68 %RANDOM
Rwork0.1647 40624 --
obs0.1669 42619 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.99 Å2
Refinement stepCycle: LAST / Resolution: 1.82→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 55 580 4721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714226
X-RAY DIFFRACTIONf_angle_d0.94175737
X-RAY DIFFRACTIONf_chiral_restr0.0603666
X-RAY DIFFRACTIONf_plane_restr0.009748
X-RAY DIFFRACTIONf_dihedral_angle_d16.46851550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.34041140.32712315X-RAY DIFFRACTION78.76
1.86-1.910.32361380.26762789X-RAY DIFFRACTION96.06
1.91-1.960.25641410.23052870X-RAY DIFFRACTION98.46
1.96-2.030.27941440.2012904X-RAY DIFFRACTION99.32
2.03-2.10.24921440.18812917X-RAY DIFFRACTION99.58
2.1-2.180.25651420.18392901X-RAY DIFFRACTION99.15
2.18-2.280.25011450.17612963X-RAY DIFFRACTION99.78
2.28-2.40.27051420.16512902X-RAY DIFFRACTION99.67
2.4-2.550.23481450.16492973X-RAY DIFFRACTION99.9
2.55-2.750.21451450.15972926X-RAY DIFFRACTION99.35
2.75-3.030.20691450.16082995X-RAY DIFFRACTION99.78
3.03-3.470.20631460.14562971X-RAY DIFFRACTION99.33
3.47-4.360.15671480.13163024X-RAY DIFFRACTION99.56
4.37-42.410.18331560.1583174X-RAY DIFFRACTION98.84
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)
13.87143492748-4.124736696193.170135501697.88726804955-1.863378360694.98719274660.1436803923910.4109318154470.185431444502-0.729709670467-0.219152429340.6155228121350.0255383499275-0.330802366756-0.1046538481360.34258488806-0.05937159779570.02098982105230.281562464422-0.01148060662190.3275023875841.4255027609427.158752301213.0224678533
23.8486893224-2.065926018250.3280980714226.47807441229-1.207750439132.59643479772-0.05174559884430.108042965559-0.07768975519140.0788291903698-0.05973991243730.5862779273560.0230415291793-0.1549744907630.09051748623560.199583650053-0.0206402131791-0.0008105544700480.224400409788-0.06447398209940.2361525425120.93403288934129.009966842617.4025942371
34.882844750292.32431270636-3.970913668825.12434650667-3.17191780498.683628331190.0816360639111-0.08553317456420.1388013313440.2922101810370.04816699536190.0248267637013-0.156276001355-0.198233749318-0.1297764678220.1966836340270.0132527393857-0.0359761051070.207225984326-0.03831322206990.2321899611069.5047920827336.993135319818.6659286538
41.57238229101-0.26558259504-0.2754214731413.731800021592.787693325514.920910474260.04550468108840.06739552628870.0732276231991-0.04433769132240.0312500208165-0.169471652074-0.06074295325120.0827298627641-0.07920583553540.209165556758-0.01961223589090.004279190099880.1749275312780.03740072309470.22120557503421.013713093334.79940664718.68880391045
52.44652067250.6832455088440.4761385225864.261466385771.165032272482.768557846970.0264875514114-0.0337262896434-0.0621251387864-0.047771274837-0.0121578447982-0.2293606717270.0416812643020.0583813389421-0.01837990722130.1562174868210.02430206411320.02105175824740.1076963276380.01905737204320.13686224919718.69325380119.63815245526.8983022919
62.27452914948-2.6324673234-1.991781393618.80814882977-0.2397088231942.8605031556-0.0625048815151-0.607336314397-0.2901993045520.390941736020.160508845329-0.283174581110.1148040084820.199823595069-0.08902741006510.3419982999960.00735664748341-0.01136869444770.2247407908790.01359214046340.16481025389419.584915185510.315477437518.365178735
79.297930581425.97082738626-4.493493600745.349531463-4.088155788896.265172676220.240034276417-0.340786664777-0.2027035749220.234851285709-0.292183563274-0.1223214202820.2985516805610.009870141063510.04149684395680.2989488315410.01116022615060.02303309916680.170169570218-0.04965691150220.20498487513511.7487421546-11.41319187963.70412801485
89.550279266756.96856233092-4.105776322935.65525706769-4.541342685836.89901115063-0.0655887281652-0.447922470964-0.187113737085-0.00733425896608-0.1002780105780.4527406259940.349227174006-0.2382223824370.1082569165330.2019092666530.00143140001167-0.01830575055870.271643150726-0.05096792556270.255980201575.56389335588-13.4312830006-1.56162955881
91.94046668167-0.3946742053470.5047996090215.11456921451-1.724219692112.360763301790.100709007943-0.0460478937722-0.167622604212-0.06962597475530.05596677744610.09451502911310.05582577139160.0962100257032-0.1606166626340.1726366808840.000942862063890.01473083336580.236049905652-0.01755029962810.25337959956915.0085939342-18.06864350362.07820381159
105.552575745581.081406720252.15344438092.26070378191.754271199015.67880086036-0.04943779195920.107796181104-0.273223988766-0.1707562372570.119989460413-0.1449620728810.0687323977170.154348893912-0.06097258610020.1542474391140.002440771090560.0289018728430.129231800387-0.006917999000830.19757622947425.9710668339-18.2448485285-0.987196853152
112.70015954091-1.13265953371-0.9337674696592.353499033280.509495083041.96896777806-0.0870123697309-0.161228493513-0.04963647135450.2381256112510.0336836103434-0.07639708999120.038898114740.141296014670.04761948730510.205591846603-0.0192391003947-0.02848469496070.1843322313740.007449631726780.21641270326129.7101829361-5.658112123312.8314592455
124.20205509792-0.8404811082620.9921015263044.878242007661.376735976262.85517823546-0.05142085093340.1072808657240.112671847554-0.1704507622620.0625265804187-0.0546946917592-0.04859875425880.146122786952-0.003586469499080.1759374302940.00350591190233-7.84435779259E-60.1520723021990.00685669376780.14444950221620.48106283895.461477899963.37612379563
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 25 )AA1 - 251 - 25
22chain 'A' and (resid 26 through 77 )AA26 - 7726 - 77
33chain 'A' and (resid 78 through 115 )AA78 - 11578 - 115
44chain 'A' and (resid 116 through 187 )AA116 - 187116 - 187
55chain 'A' and (resid 188 through 252 )AA188 - 252188 - 252
66chain 'A' and (resid 253 through 270 )AA253 - 270253 - 270
77chain 'B' and (resid 1 through 21 )BC1 - 211 - 21
88chain 'B' and (resid 22 through 38 )BC22 - 3822 - 38
99chain 'B' and (resid 39 through 77 )BC39 - 7739 - 77
1010chain 'B' and (resid 78 through 130 )BC78 - 13078 - 130
1111chain 'B' and (resid 131 through 229 )BC131 - 229131 - 229
1212chain 'B' and (resid 230 through 270 )BC230 - 270230 - 270

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