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- PDB-3rgg: Crystal structure of Treponema denticola PurE bound to AIR -

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Basic information

Entry
Database: PDB / ID: 3rgg
TitleCrystal structure of Treponema denticola PurE bound to AIR
ComponentsPhosphoribosylaminoimidazole carboxylase, PurE protein
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
5-AMINOIMIDAZOLE RIBONUCLEOTIDE / Phosphoribosylaminoimidazole carboxylase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMathews, I.I. / Starks, C.M. / Kappock, T.J.
CitationJournal: Biochemistry / Year: 2011
Title: Treponema denticola PurE Is a Bacterial AIR Carboxylase.
Authors: Tranchimand, S. / Starks, C.M. / Mathews, I.I. / Hockings, S.C. / Kappock, T.J.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase, PurE protein
B: Phosphoribosylaminoimidazole carboxylase, PurE protein
C: Phosphoribosylaminoimidazole carboxylase, PurE protein
D: Phosphoribosylaminoimidazole carboxylase, PurE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2288
Polymers69,0484
Non-polymers1,1814
Water5,098283
1
A: Phosphoribosylaminoimidazole carboxylase, PurE protein
B: Phosphoribosylaminoimidazole carboxylase, PurE protein
C: Phosphoribosylaminoimidazole carboxylase, PurE protein
D: Phosphoribosylaminoimidazole carboxylase, PurE protein
hetero molecules

A: Phosphoribosylaminoimidazole carboxylase, PurE protein
B: Phosphoribosylaminoimidazole carboxylase, PurE protein
C: Phosphoribosylaminoimidazole carboxylase, PurE protein
D: Phosphoribosylaminoimidazole carboxylase, PurE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,45716
Polymers138,0958
Non-polymers2,3618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area37180 Å2
ΔGint-119 kcal/mol
Surface area39830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.390, 155.130, 88.140
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
11C-218-

HOH

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Components

#1: Protein
Phosphoribosylaminoimidazole carboxylase, PurE protein /


Mass: 17261.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: PurE, TDE_0687 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q73PV9, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE / 5-Aminoimidazole ribotide


Mass: 295.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14N3O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→37.1 Å / Num. all: 51257 / Num. obs: 51257 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.064 / Net I/σ(I): 20
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3520 / Rsym value: 0.865 / % possible all: 92.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native coordinate

Resolution: 1.82→37.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.459 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22155 2607 5.1 %RANDOM
Rwork0.18816 ---
obs0.18985 48510 98.34 %-
all-48510 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--2.22 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.82→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 76 283 5062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224873
X-RAY DIFFRACTIONr_bond_other_d0.0010.023338
X-RAY DIFFRACTIONr_angle_refined_deg1.6742.0116590
X-RAY DIFFRACTIONr_angle_other_deg0.9838200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95123.988173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9061524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.53107
X-RAY DIFFRACTIONr_mcbond_other0.2161.51254
X-RAY DIFFRACTIONr_mcangle_it1.21224985
X-RAY DIFFRACTIONr_scbond_it2.18331766
X-RAY DIFFRACTIONr_scangle_it3.3624.51604
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 197 -
Rwork0.38 3313 -
obs--92.1 %
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)
12.0488-0.2221-0.10740.7982-0.17181.83960.11420.04170.6702-0.08610.0445-0.1121-0.57130.251-0.15870.2368-0.09290.0870.0448-0.0090.3118.7043-12.769419.1905
22.05820.3851-0.36170.97990.09112.1955-0.012-0.3952-0.00660.02540.0163-0.1610.20290.8602-0.00430.02830.0952-0.01230.4329-0.00770.049624.3233-43.009433.9321
31.954-0.38290.05141.1551-0.28522.5259-0.10040.2273-0.4992-0.15580.0477-0.040.82620.06290.05270.331-0.01050.06770.0399-0.07430.20562.1712-64.565613.0178
41.4678-0.03630.04871.1342-0.19362.33880.07040.55960.1308-0.2039-0.0289-0.0270.0485-0.4261-0.04150.04240.02650.00620.36640.05950.0188-13.5019-34.046-1.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 157
2X-RAY DIFFRACTION2B2 - 157
3X-RAY DIFFRACTION3C2 - 156
4X-RAY DIFFRACTION4D1 - 156

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