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- PDB-6q62: Xanthomonas albilineans Dihydropteroate synthase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6q62
TitleXanthomonas albilineans Dihydropteroate synthase in complex with (indole-2-carboxylic acid) and (6-chloroguanine)
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Complex / FBDD / Fragments
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-chloroguanine / 1H-indole-2-carboxylic acid / DI(HYDROXYETHYL)ETHER / Dihydropteroate synthase
Similarity search - Component
Biological speciesXanthomonas albilineans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOliveira, A.A. / Hyvonen, M. / Guido, R.V.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation2017/17816-4 Brazil
CitationJournal: To Be Published
Title: Xanthomonas albilineans Dihydropteroate synthase in complex with (indole-2-carboxylic acid) and (6-chloroguanine)
Authors: Oliveira, A.A. / Hyvonen, M. / Guido, R.V.C.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase
C: Dihydropteroate synthase
B: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,92226
Polymers127,5344
Non-polymers2,38822
Water14,070781
1
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,87212
Polymers63,7672
Non-polymers1,10510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-85 kcal/mol
Surface area21710 Å2
MethodPISA
2
C: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,05014
Polymers63,7672
Non-polymers1,28312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-73 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.382, 74.553, 89.299
Angle α, β, γ (deg.)90.00, 101.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ACBD

#1: Protein
Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 31883.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas albilineans (bacteria) / Gene: folP, XALc_1165 / Plasmid: pETTrx / Details (production host): Thioredoxin + 6xHis / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7Lac / References: UniProt: D2UDM3, dihydropteroate synthase

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Non-polymers , 6 types, 803 molecules

#2: Chemical
ChemComp-6GU / 6-chloroguanine / 6-chloro-9H-purin-2-amine


Mass: 169.572 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4ClN5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ICB / 1H-indole-2-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.11 Å3/Da / Density % sol: 43 % / Description: Monoclinic
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3.350, Li2SO4, Bis-tris

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→54 Å / Num. obs: 137050 / % possible obs: 81.84 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08753 / Rpim(I) all: 0.03612 / Rrim(I) all: 0.09483 / Net I/σ(I): 12.14
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 5075 / CC1/2: 0.75 / % possible all: 36.32

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DAY

6day


Resolution: 1.5→42.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6098 5.02 %RANDOM
Rwork0.211 ---
obs0.213 121443 71.7 %-
Displacement parametersBiso mean: 23.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.0736 Å20 Å20.1292 Å2
2--0.2034 Å20 Å2
3----0.1297 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.5→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7778 0 147 781 8706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018082HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111019HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1447HARMONIC5
X-RAY DIFFRACTIONt_it8082HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion14.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1074SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10090SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2707 111 4.58 %
Rwork0.2316 2315 -
all0.2335 2426 -
obs--19.44 %

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