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- PDB-6ucz: Crystal structure of dihydropteroate synthase from Anaplasma phag... -

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Basic information

Entry
Database: PDB / ID: 6ucz
TitleCrystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / SSGCID / PMM / dihydropteroate synthase / ptp / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 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
ACETATE ION / CITRIC ACID / PTERIN-6-YL-METHYL-MONOPHOSPHATE / Dihydropteroate synthase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate
Authors: Bolejack, M.J. / Delker, S.L. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Oct 11, 2023Group: 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
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)64,81812
Polymers63,8432
Non-polymers97410
Water4,720262
1
A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4695
Polymers31,9221
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3497
Polymers31,9221
Non-polymers4276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.830, 81.480, 71.170
Angle α, β, γ (deg.)90.000, 102.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 31921.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Gene: WSQ_01200, folP / Plasmid: AnphA.01019.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5PWL8, dihydropteroate synthase

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Non-polymers , 6 types, 272 molecules

#2: Chemical ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE


Mass: 273.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N5O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1:1 20 mg/mL AnphA.01019.a.A1.PW27052 in 2.5 mM Ptp, 100 mM sodium cacodylate/HCl, pH 6.5, 20% w/v PEG8000, 200 mM magnesium acetate against 100 mM sodium citrate tribasic/HCl, pH 5.5, 20% ...Details: 1:1 20 mg/mL AnphA.01019.a.A1.PW27052 in 2.5 mM Ptp, 100 mM sodium cacodylate/HCl, pH 6.5, 20% w/v PEG8000, 200 mM magnesium acetate against 100 mM sodium citrate tribasic/HCl, pH 5.5, 20% w/v PEG3000, cryoprotectant: 20% ethylene glycol, 2.5 mM Ptp, tray 311087h9, puck tni6-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2019 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→38.75 Å / Num. obs: 36233 / % possible obs: 98.2 % / Redundancy: 3.659 % / Biso Wilson estimate: 34.394 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Χ2: 1.023 / Net I/σ(I): 19.42 / Num. measured all: 132591 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.052.7150.3422.916218272222900.9120.42584.1
2.05-2.112.9820.26347457264725010.9540.31994.5
2.11-2.173.5060.254.798940255325500.9630.29699.9
2.17-2.243.8170.2196.129481249424840.9770.25699.6
2.24-2.313.8170.1737.469320243924420.9850.201100
2.31-2.393.8240.148.998910233223300.990.16399.9
2.39-2.483.8180.12110.298599225822520.9910.14199.7
2.48-2.583.8280.09812.388407220321960.9950.11499.7
2.58-2.73.8320.07915.278012208720910.9960.092100
2.7-2.833.8230.0717.757603199619890.9960.08299.6
2.83-2.983.8150.05721.167256190719020.9970.06699.7
2.98-3.163.8120.04625.586865180518010.9980.05399.8
3.16-3.383.8120.03432.346485170317010.9990.0499.9
3.38-3.653.8130.0336.985975157015670.9990.03599.8
3.65-43.7810.02544.445532147014630.9990.02999.5
4-4.473.7870.02149.124995132413190.9990.02599.6
4.47-5.163.8090.0251.84407115711570.9990.023100
5.16-6.323.7760.02249.0837579979950.9990.02599.8
6.32-8.943.7040.01952.228527737700.9990.02299.6
8.94-38.753.510.01656.9515204434330.9990.01997.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OMZ

6omz


Resolution: 2→38.75 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.74
RfactorNum. reflection% reflection
Rfree0.1975 1985 5.48 %
Rwork0.1619 --
obs0.1639 36196 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.7 Å2 / Biso mean: 39.8793 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 2→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 66 270 4268
Biso mean--49.73 45.45 -
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.26861080.23292100220884
2.05-2.110.24441200.20832325244594
2.11-2.170.19921420.193824632605100
2.17-2.240.24491550.181524502605100
2.24-2.320.25111430.171225112654100
2.32-2.410.21571240.168824652589100
2.41-2.520.21031480.165224622610100
2.52-2.650.20291490.167424842633100
2.65-2.820.22291490.168224692618100
2.82-3.040.19981460.171824832629100
3.04-3.340.1921530.157724692622100
3.34-3.820.18011710.143624752646100
3.82-4.820.17431410.138525042645100
4.82-38.750.17841360.160725512687100
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)
13.6360.9146-0.41813.22210.01496.78920.0937-0.26410.25380.239-0.1-0.2321-0.35270.50670.02050.4015-0.0324-0.03890.2349-0.06920.271524.859727.1642-26.9831
21.5460.1193-0.72352.7273-0.05644.8504-0.0146-0.1324-0.0014-0.0338-0.04430.18370.1292-0.18820.070.231-0.0236-0.00330.1918-0.02520.166514.875413.2724-32.4126
37.1179-2.1746-5.04264.1091.71769.26130.03190.08710.14210.1750.0282-0.6735-0.24160.8739-0.08980.4119-0.0643-0.05920.28060.00740.240519.60511.01822.3217
42.6537-0.07990.15261.9783-0.27223.68460.02670.12780.0531-0.05560.01660.08790.0080.1546-0.07550.36850.01350.01780.1625-0.00730.15659.139-2.6175-5.6098
51.7759-0.19840.99325.39723.22424.1567-0.10150.10310.1726-0.4989-0.23030.5409-0.5055-0.25860.27860.343-0.0007-0.00910.2093-0.01790.2076-7.54189.4861-1.033
62.4354-0.01580.91560.61030.78953.6709-0.0267-0.02540.15370.264-0.02130.08380.05-0.02240.04670.43140.00770.03260.1547-0.00190.19152.48078.164412.6091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 142 )A28 - 142
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 292 )A143 - 292
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 64 )B28 - 64
4X-RAY DIFFRACTION4chain 'B' and (resid 65 through 157 )B65 - 157
5X-RAY DIFFRACTION5chain 'B' and (resid 158 through 222 )B158 - 222
6X-RAY DIFFRACTION6chain 'B' and (resid 223 through 292 )B223 - 292

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