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- PDB-5umg: Crystal structure of dihydropteroate synthase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 5umg
TitleCrystal structure of dihydropteroate synthase from Klebsiella pneumoniae subsp.
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / dihydropteroate synthase
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
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
Dihydropteroate synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsChang, C. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of dihydropteroate synthase from Klebsiella pneumoniae subsp.
Authors: Chang, C. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8663
Polymers61,7742
Non-polymers921
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.313, 78.313, 150.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21B-423-

HOH

31B-429-

HOH

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Components

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 30887.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: folP, KPN_03587 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A6TEJ6, dihydropteroate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M Lithium Chloride, 0.1 M Tris-Cl, 32% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.6→44.582 Å / Num. obs: 14823 / % possible obs: 98.2 % / Redundancy: 11 % / Biso Wilson estimate: 40.75 Å2 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.052 / Rrim(I) all: 0.179 / Χ2: 0.904 / Net I/σ(I): 5.2 / Num. measured all: 162490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.61.1750.6560.5091.2860.87688.9
2.64-2.697.11.0130.7490.3781.0850.90890
2.69-2.748.20.9450.7860.321.0010.90293.3
2.74-2.88.91.040.7920.3421.0980.90296.1
2.8-2.869.60.9250.8430.2950.9740.91898.1
2.86-2.9310.10.8990.8240.2870.9460.91698.7
2.93-310.70.8370.90.2590.8770.92299.6
3-3.0810.90.7670.9060.2380.8040.999.7
3.08-3.1711.40.6220.9510.190.6510.89100
3.17-3.2810.60.5140.9490.1630.540.929100
3.28-3.3912.90.3930.9760.1130.410.935100
3.39-3.5313.10.3110.9860.0890.3230.967100
3.53-3.69130.2460.9710.0710.2570.972100
3.69-3.8812.90.1940.9910.0560.2020.951100
3.88-4.1312.50.1550.9920.0450.1610.906100
4.13-4.4511.80.1210.9910.0360.1260.907100
4.45-4.8913.10.1080.9950.0310.1130.88699.9
4.89-5.612.50.1060.9950.030.110.849100
5.6-7.0511.50.1030.9920.0310.1080.873100
7.05-5010.90.0660.9950.0210.070.75299.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.601→44.582 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2654 686 5.07 %
Rwork0.2079 --
obs0.2109 13536 89.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.7 Å2 / Biso mean: 45.9809 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 2.601→44.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 6 52 3862
Biso mean--66.26 37.59 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023892
X-RAY DIFFRACTIONf_angle_d0.4115261
X-RAY DIFFRACTIONf_chiral_restr0.038624
X-RAY DIFFRACTIONf_plane_restr0.003679
X-RAY DIFFRACTIONf_dihedral_angle_d11.1742345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6006-2.70480.3968950.27671728182359
2.7048-2.82780.3028980.27482195229375
2.8278-2.97690.38491340.28162449258385
2.9769-3.16340.31481370.24592659279691
3.1634-3.40750.26671410.2192891303299
3.4075-3.75030.24351790.197628673046100
3.7503-4.29260.24591600.182828783038100
4.2926-5.40670.23881490.171928803029100
5.4067-44.5890.23751580.19932895305399
Refinement TLS params.Method: refined / Origin x: 39.0149 Å / Origin y: 37.4656 Å / Origin z: 54.8975 Å
111213212223313233
T0.1396 Å2-0.1031 Å2-0.1398 Å2-0.0075 Å2-0.0676 Å2--0.0159 Å2
L0.32 °2-0.0267 °20.0291 °2-0.1007 °2-0.0601 °2--0.4309 °2
S-0.1606 Å °-0.0068 Å °-0.1227 Å °-0.0172 Å °-0.1194 Å °0.0484 Å °0.1168 Å °0.2274 Å °-0.4045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 282
2X-RAY DIFFRACTION1allB1 - 282
3X-RAY DIFFRACTION1allW1 - 52
4X-RAY DIFFRACTION1allC1

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