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- PDB-5c5d: Crystal structure of Treponema denticola PurE2-S38D -

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Basic information

Entry
Database: PDB / ID: 5c5d
TitleCrystal structure of Treponema denticola PurE2-S38D
Componentsphosphoribosylaminoimidazole carboxylase
KeywordsLYASE / purine biosynthesis / carboxylase
Function / homology
Function and homology information


phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
Class II PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylaminoimidazole carboxylase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsSullivan, K.L. / Kappock, T.J.
CitationJournal: To be published
Title: Function of conserved residues in the class II PurE active site
Authors: Sullivan, K.L. / Mathews, I.I. / Kappock, T.j.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphoribosylaminoimidazole carboxylase
B: phosphoribosylaminoimidazole carboxylase
C: phosphoribosylaminoimidazole carboxylase
D: phosphoribosylaminoimidazole carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2949
Polymers68,9844
Non-polymers3105
Water10,287571
1
A: phosphoribosylaminoimidazole carboxylase
B: phosphoribosylaminoimidazole carboxylase
C: phosphoribosylaminoimidazole carboxylase
D: phosphoribosylaminoimidazole carboxylase
hetero molecules

A: phosphoribosylaminoimidazole carboxylase
B: phosphoribosylaminoimidazole carboxylase
C: phosphoribosylaminoimidazole carboxylase
D: phosphoribosylaminoimidazole carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,58818
Polymers137,9678
Non-polymers62110
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area34420 Å2
ΔGint-115 kcal/mol
Surface area42970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.084, 154.958, 89.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

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Components

#1: Protein
phosphoribosylaminoimidazole carboxylase / AIR carboxylase / 5-aminoimidazole ribonucleotide carboxylase


Mass: 17245.883 Da / Num. of mol.: 4 / Mutation: S38D
Source method: isolated from a genetically manipulated source
Details: Synthetic gene
Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) (bacteria)
Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: purE, TDE_0687 / Plasmid: pET23a / Details (production host): pJK644 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q73PV9, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14-16% (w/v) PEG 1000, 0.1 M magnesium chloride, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 64883 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 21.54 Å2 / Rsym value: 0.077 / Net I/σ(I): 55.32
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 5.26 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3rgg

3rgg


Resolution: 1.69→44.565 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3312 5.11 %same as 3rgg
Rwork0.1545 ---
obs0.1563 64843 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→44.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 20 571 5391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114930
X-RAY DIFFRACTIONf_angle_d1.296649
X-RAY DIFFRACTIONf_dihedral_angle_d12.121870
X-RAY DIFFRACTIONf_chiral_restr0.053760
X-RAY DIFFRACTIONf_plane_restr0.007849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.71410.21181150.20022150X-RAY DIFFRACTION84
1.7141-1.73970.25171380.18772534X-RAY DIFFRACTION100
1.7397-1.76690.23521350.18182587X-RAY DIFFRACTION100
1.7669-1.79590.21061310.18412538X-RAY DIFFRACTION100
1.7959-1.82680.20931480.16522564X-RAY DIFFRACTION100
1.8268-1.860.19521490.16922530X-RAY DIFFRACTION100
1.86-1.89580.18861560.16782559X-RAY DIFFRACTION100
1.8958-1.93450.22881420.16712544X-RAY DIFFRACTION100
1.9345-1.97660.21461380.1632554X-RAY DIFFRACTION100
1.9766-2.02260.2011410.15792562X-RAY DIFFRACTION100
2.0226-2.07310.18141510.16142554X-RAY DIFFRACTION100
2.0731-2.12920.20261280.16542577X-RAY DIFFRACTION100
2.1292-2.19180.19481370.16072587X-RAY DIFFRACTION100
2.1918-2.26260.17611360.1522563X-RAY DIFFRACTION100
2.2626-2.34350.21891360.15632586X-RAY DIFFRACTION100
2.3435-2.43730.19121420.16052558X-RAY DIFFRACTION100
2.4373-2.54820.20991320.1732618X-RAY DIFFRACTION100
2.5482-2.68250.17061210.16342602X-RAY DIFFRACTION100
2.6825-2.85060.21181350.16362592X-RAY DIFFRACTION100
2.8506-3.07060.18571370.16092593X-RAY DIFFRACTION100
3.0706-3.37950.20161460.15582607X-RAY DIFFRACTION100
3.3795-3.86830.19091480.13792625X-RAY DIFFRACTION100
3.8683-4.87270.15041500.12742626X-RAY DIFFRACTION100
4.8727-44.58050.17641200.14762721X-RAY DIFFRACTION97
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)
10.3189-0.241-0.02740.4466-0.26970.3679-0.36190.09830.81170.06830.0263-0.2385-0.48480.28160.04310.3717-0.1325-0.21360.11120.13440.66718.4109-12.39218.484
21.6310.28580.49051.15140.28841.1435-0.01360.10920.05580.04350.0819-0.1820.05590.2394-0.06390.1022-0.0018-0.01080.2114-0.05050.168224.6979-41.926834.3469
31.2732-0.22320.24090.99510.05711.08930.04770.0931-0.0737-0.08530.0621-0.08090.21850.0609-0.0890.15310.0165-0.00430.0979-0.01530.13283.1278-64.458813.5956
41.0746-0.32190.31641.4913-0.23710.93250.0530.22090.218-0.1642-0.0579-0.06230.03990.0060.00680.12380.01090.00790.22640.06590.1602-12.7279-34.7156-1.9947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 159 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 158 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 158 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 159 )

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