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- PDB-11te: Crystal Structure of ATP phosphoribosyltransferase from Bordetell... -

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Basic information

Entry
Database: PDB / ID: 11te
TitleCrystal Structure of ATP phosphoribosyltransferase from Bordetella pertussis
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ATP phosphoribosyltransferase / Bordetella pertussis
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature.
Similarity search - Domain/homology
ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of ATP phosphoribosyltransferase from Bordetella pertussis
Authors: Ung, A.R. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionMar 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0196
Polymers24,6031
Non-polymers4165
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,03812
Polymers49,2072
Non-polymers83110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4390 Å2
ΔGint-123 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.269, 83.269, 63.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRT / ATP-PRTase


Mass: 24603.416 Da / Num. of mol.: 1 / Fragment: A5-A223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: hisG, BP3767 / Plasmid: BopeA.19523.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7VSZ2, ATP phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Proplex G4: 100 mM Tris, pH 8.0, 2 M Ammonium sulfate. BopeA.19523.a.B2.PW39511 at 21.3 mg/mL. 2 mM AMP and 4 mM MgCl2 added prior to crystallization but no electron density was observed for ...Details: Proplex G4: 100 mM Tris, pH 8.0, 2 M Ammonium sulfate. BopeA.19523.a.B2.PW39511 at 21.3 mg/mL. 2 mM AMP and 4 mM MgCl2 added prior to crystallization but no electron density was observed for these. plate 20737 G4 drop 2, Puck: PSL-1515, Cryo: 70% crystallant + 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 22, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→43.26 Å / Num. obs: 33158 / % possible obs: 100 % / Redundancy: 26.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.028 / Rrim(I) all: 0.142 / Χ2: 1.35 / Net I/σ(I): 22.1 / Num. measured all: 866284
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 26.1 % / Rmerge(I) obs: 2.934 / Num. measured all: 41677 / Num. unique obs: 1595 / CC1/2: 0.595 / Rpim(I) all: 0.583 / Rrim(I) all: 2.992 / Χ2: 0.93 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.26 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 1628 4.92 %
Rwork0.1934 --
obs0.1947 33087 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 22 121 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091617
X-RAY DIFFRACTIONf_angle_d1.0382206
X-RAY DIFFRACTIONf_dihedral_angle_d13.793593
X-RAY DIFFRACTIONf_chiral_restr0.062267
X-RAY DIFFRACTIONf_plane_restr0.01283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.29471110.26982596X-RAY DIFFRACTION100
1.6-1.650.27821290.23742569X-RAY DIFFRACTION100
1.65-1.710.28041490.23682556X-RAY DIFFRACTION100
1.71-1.770.28241540.26122585X-RAY DIFFRACTION100
1.77-1.860.24541400.21182573X-RAY DIFFRACTION100
1.86-1.950.22921450.1912580X-RAY DIFFRACTION100
1.95-2.080.22211310.182606X-RAY DIFFRACTION100
2.08-2.240.24581280.18362621X-RAY DIFFRACTION100
2.24-2.460.21061340.17442636X-RAY DIFFRACTION100
2.46-2.820.20471190.19112654X-RAY DIFFRACTION100
2.82-3.550.20591400.17942675X-RAY DIFFRACTION100
3.55-43.260.20441480.19612808X-RAY DIFFRACTION99
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)
13.8384-0.2742-1.34533.576-0.3853.75850.14630.5590.4487-0.18350.06560.597-0.4722-0.88460.02790.21040.0924-0.03320.30220.07860.26010.3095-19.24773.9972
24.25224.41971.46896.02081.77690.8083-0.16850.1414-0.2384-0.4090.1833-0.3204-0.08890.03750.00590.2295-0.01180.02420.19360.01490.148221.9369-13.53792.0685
31.7761.96770.99554.16651.42213.5669-0.080.06330.115-0.17220.00650.1505-0.00860.02880.04270.1232-0.00780.00490.14090.00510.128527.4167-7.99867.785
44.1039-0.68391.29515.2057-1.14924.913-0.08970.5904-0.108-0.34820.05340.48920.0815-0.3047-0.03040.2742-0.0351-0.08060.35170.00270.20863.1407-24.353-6.7809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 221 )

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