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- PDB-5clj: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -

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Basic information

Entry
Database: PDB / ID: 5clj
TitleStructure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) H59N from the acidophilic bacterium Acetobacter aceti, complexed with AIR (5-aminoimidazole ribonucleotide) and CO2
ComponentsN5-carboxyaminoimidazole ribonucleotide mutase
KeywordsISOMERASE / acidophile / purine biosynthesis / PurE
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
: / Class I 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 / CITRIC ACID / CARBON DIOXIDE / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesAcetobacter aceti 1023 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsStarks, C.M. / Kappock, T.J.
Funding support United States, 3items
OrganizationGrant numberCountry
Herman Frasch Foundation531-HF02 United States
National Science Foundation (NSF, United States)MCB0347250 United States
Department of Education200A010213 United States
Citation
Journal: To Be Published
Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE
Authors: Sullivan, K.L. / Tranchimand, S. / Kappock, T.J.
#1: Journal: Biochemistry / Year: 2006
Title: Biochemical and structural studies of N5-carboxyaminoimidazole ribonucleotide mutase from the acidophilic bacterium Acetobacter aceti.
Authors: Constantine, C.Z. / Starks, C.M. / Mill, C.P. / Ransome, A.E. / Karpowicz, S.J. / Francois, J.A. / Goodman, R.A. / Kappock, T.J.
#2: Journal: Biochemistry / Year: 2007
Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE
Authors: Hoskins, A.A. / Morar, M. / Kappock, T.J. / Mathews, I.I. / Zaugg, J.B. / Barder, T.E. / Peng, P. / Okamoto, A. / Ealick, S.E. / Stubbe, J.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3116
Polymers37,7172
Non-polymers5934
Water6,053336
1
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,24324
Polymers150,8698
Non-polymers2,37416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area37140 Å2
ΔGint-123 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.683, 98.683, 165.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-433-

HOH

31B-443-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase


Mass: 18858.666 Da / Num. of mol.: 2 / Mutation: H59N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Details (production host): pJK283 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus-RIL
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

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Non-polymers , 5 types, 340 molecules

#2: Chemical ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE


Mass: 295.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O7P
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 22% PEG 4000, 190 mM ammonium acetate, 90 mM sodium citrate

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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: Jul 29, 2005
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 33561 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.05 / Net I/σ(I): 24.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.3 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ycb chain A

4ycb


Resolution: 1.85→42.386 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1599 4.76 %Random selection
Rwork0.1506 ---
obs0.1521 33561 95.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→42.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 39 336 2685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092510
X-RAY DIFFRACTIONf_angle_d1.0653453
X-RAY DIFFRACTIONf_dihedral_angle_d13.085922
X-RAY DIFFRACTIONf_chiral_restr0.045416
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90970.33711080.30952305X-RAY DIFFRACTION76
1.9097-1.9780.2791290.25422661X-RAY DIFFRACTION89
1.978-2.05720.26651270.2182898X-RAY DIFFRACTION95
2.0572-2.15080.21781670.19032889X-RAY DIFFRACTION97
2.1508-2.26420.21861510.16522927X-RAY DIFFRACTION97
2.2642-2.4060.17911600.14582952X-RAY DIFFRACTION98
2.406-2.59180.18491650.13972941X-RAY DIFFRACTION98
2.5918-2.85250.19841320.13953036X-RAY DIFFRACTION99
2.8525-3.26520.16411370.13593047X-RAY DIFFRACTION99
3.2652-4.11320.15821530.12523091X-RAY DIFFRACTION99
4.1132-42.39670.14231700.12653215X-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)
12.7218-0.7465-0.96030.8547-1.65325.9860.0897-0.51390.45220.3221-0.2949-0.1082-0.3220.09350.21380.19660.0298-0.04030.2224-0.06250.3079-6.370929.95635.9764
24.97194.6135-0.79474.9474-0.93580.84750.1496-0.41550.07320.2217-0.2042-0.13830.01530.0610.03120.23480.0216-0.01950.273-0.04220.2151-1.142622.828141.2652
34.83442.25010.98832.38620.16570.2981-0.0837-0.03120.3756-0.00960.03130.1523-0.05770.01890.05160.18220.0199-0.00740.1939-0.04870.1855-8.307827.450136.391
45.65643.9925-1.87924.826-2.04721.2101-0.11090.18940.86640.06220.27930.8323-0.176-0.2139-0.13450.20690.0413-0.04670.2014-0.01510.3356-16.971630.075328.6479
52.4489-0.62680.24091.42020.89532.4613-0.0280.04830.3048-0.1092-0.11710.0066-0.1754-0.09740.1140.1728-0.0022-0.02980.162-0.01170.2363-8.053726.094927.4973
60.9906-2.8084-0.09617.9620.27270.00930.0628-1.4184-0.86221.1953-0.1652-0.14250.4941-0.41220.53680.4522-0.1234-0.01210.44590.14140.2805-4.64015.733634.7847
72.75211.51330.56923.12961.30981.3914-0.07-0.00710.2151-0.021-0.01830.0029-0.06070.01190.08380.14280.0167-0.01270.15430.00520.14770.770722.457126.7473
87.8492-7.79133.46588.2832-3.92112.17290.30890.23760.2078-0.5047-0.2901-0.14720.16680.1955-0.01640.1982-0.0348-0.03050.2036-0.04020.274514.631231.962135.2368
98.2462-6.50070.78515.3232-1.36232.8594-0.1402-0.64610.13361.28520.108-0.58530.31570.3656-0.01750.40350.0215-0.10680.2814-0.06420.328223.827114.252143.6929
102.44330.5602-0.44270.13290.01453.19510.14350.34990.3425-0.6156-0.382-0.4125-0.29110.07080.22050.2909-0.0349-0.02110.25830.10140.2812.767328.468111.8648
118.0221-6.3619-1.4155.81971.49810.79740.31610.6639-0.1189-0.585-0.28060.3989-0.074-0.1398-0.04880.2974-0.0108-0.03920.31970.05580.17016.410322.54676.3211
121.9601-0.34660.12581.72120.30450.5589-0.00740.1070.3174-0.057-0.0578-0.2148-0.07130.11960.06850.2345-0.0409-0.00570.21120.05160.198515.649725.015817.7447
133.20630.64594.37322.7278-2.33579.94780.02930.5497-0.0679-1.0432-0.0502-0.1920.0990.08140.04460.29640.01290.01960.2588-0.01210.22215.91994.945212.6297
141.6534-0.87590.11674.17630.40392.03320.0120.04870.1746-0.1536-0.02290.0125-0.11040.05990.00890.1169-0.023-0.00080.15610.02450.13384.060422.077320.6798
157.41512.09434.53561.25931.68056.2215-0.1461-0.00240.4942-0.16410.17740.5184-0.5091-0.3803-0.08170.36090.0504-0.06220.30730.10810.334-7.523234.997612.5546
166.89554.27354.41553.26384.14037.6234-0.6711-0.06050.1993-1.08870.64051.0558-0.2779-0.4020.0570.4557-0.0684-0.15310.40120.07710.3171-20.651819.16763.9841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 107 )
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 154 )
8X-RAY DIFFRACTION8chain 'A' and (resid 155 through 171 )
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 30 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 46 )
12X-RAY DIFFRACTION12chain 'B' and (resid 47 through 107 )
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 114 )
14X-RAY DIFFRACTION14chain 'B' and (resid 115 through 154 )
15X-RAY DIFFRACTION15chain 'B' and (resid 155 through 171 )
16X-RAY DIFFRACTION16chain 'B' and (resid 172 through 179 )

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