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- PDB-4ycc: Structure of a single tryptophan mutant of Acetobacter aceti PurE... -

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Basic information

Entry
Database: PDB / ID: 4ycc
TitleStructure of a single tryptophan mutant of Acetobacter aceti PurE with Y154L mutation
ComponentsN5-carboxyaminoimidazole ribonucleotide mutase
KeywordsISOMERASE / acidophile / PurE / purine biosynthesis
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
ACETATE ION / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesAcetobacter aceti 1023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.257 Å
AuthorsKappock, T.J. / Sullivan, K.L.
CitationJournal: To Be Published
Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE
Authors: Sullivan, K.L. / Tranchimand, S. / Kappock, T.J.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Structure summary
Revision 1.2Sep 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: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9818
Polymers37,5092
Non-polymers4716
Water4,053225
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)151,92232
Polymers150,0378
Non-polymers1,88524
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 area35770 Å2
ΔGint-335 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.458, 99.458, 165.567
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-405-

HOH

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Components

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


Mass: 18754.623 Da / Num. of mol.: 2 / Mutation: W34F, Y154L, W165F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 30% w/v PEG 4000, 0.1 M Tris-HCl, 0.2 M lithium sulfate

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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: Dec 3, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 19655 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 26.22 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.102 / Net I/σ(I): 37.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 10.6 / % possible all: 99.6

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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: 4YCB

4ycb


Resolution: 2.257→49.729 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.171 945 4.81 %same as 4YCB
Rwork0.1276 ---
obs0.1298 19655 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.257→49.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 27 225 2546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122401
X-RAY DIFFRACTIONf_angle_d1.2353283
X-RAY DIFFRACTIONf_dihedral_angle_d12.651872
X-RAY DIFFRACTIONf_chiral_restr0.05404
X-RAY DIFFRACTIONf_plane_restr0.007425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.257-2.3760.21341230.14522601X-RAY DIFFRACTION98
2.376-2.52490.20721440.14192648X-RAY DIFFRACTION100
2.5249-2.71980.19151260.1422670X-RAY DIFFRACTION99
2.7198-2.99350.21121500.14392631X-RAY DIFFRACTION99
2.9935-3.42660.19121370.13172683X-RAY DIFFRACTION99
3.4266-4.31680.14821330.1112692X-RAY DIFFRACTION98
4.3168-49.7410.13411320.11852785X-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)
16.28270.4551-1.28372.88194.10046.3537-0.13690.32990.1921-0.22090.20770.2578-0.2418-0.05860.0070.2405-0.0007-0.02960.21780.08020.25885.800230.1854-35.8619
24.4358-5.36820.27736.8551-0.24416.24250.1980.47450.2765-0.3366-0.2215-0.28320.27290.0285-0.0260.2572-0.03840.02060.2750.03690.22430.753222.9335-41.1895
34.9653-4.67214.74125.7186-4.28394.9005-0.03940.39420.2483-0.0522-0.1534-0.1063-0.0320.27250.0830.1759-0.01210.00670.16830.01560.17767.914727.6026-36.3412
45.6087-6.8678-4.0718.72094.9193.5410.0796-0.05230.87430.07290.0233-0.693-0.2137-0.0358-0.16130.2632-0.05390.00990.23630.03130.327616.191530.4445-28.7983
53.8752-1.50010.9244.0925-0.52782.87770.0011-0.13410.29130.0615-0.0844-0.1162-0.11870.0360.07060.1713-0.00470.00930.17140.00310.13767.257226.5259-27.08
61.6858-1.47160.09282.1999-0.77283.70760.22081.1754-0.6302-1.4082-0.50180.62790.60160.2280.51310.46110.0657-0.0180.4321-0.05850.30014.57325.812-34.8563
73.2838-2.81840.54594.545-0.64761.7894-0.00050.00610.13350.042-0.093-0.1327-0.0454-0.02050.09250.141-0.03460.02090.15030.01440.1255-1.152321.8951-26.75
88.66798.69434.46769.65933.83072.64030.1824-0.1015-0.02610.2921-0.2012-0.11820.062-0.09410.01020.21720.0614-0.02110.23150.03020.2129-15.376131.8675-35.0451
99.72025.48493.29753.59381.71182.2063-0.15460.4877-0.3007-1.7320.44990.34290.3266-0.2181-0.29660.5438-0.0255-0.04150.32170.03580.2682-24.44913.7143-43.6748
108.33171.5021-1.61792.6426-4.41897.580.0144-0.450.47730.4661-0.1303-0.1942-0.1776-0.02970.19640.25430.0402-0.03110.3011-0.06780.1481-13.540527.9186-11.6595
113.7511.6633-3.31533.0638-3.53695.19270.0693-0.47030.16020.80460.0490.07140.06070.2486-0.01910.32250.0541-0.03320.308-0.0510.1739-6.807422.3436-6.2018
122.66650.6412-0.23022.68580.2991.42430.0301-0.00690.21570.1457-0.00710.2651-0.1202-0.1694-0.02490.26550.04010.00770.2186-0.0120.1758-16.296824.184-17.5102
132.12141.23962.62941.50682.64244.80210.5753-1.3414-0.82321.6725-0.3851-0.69940.3790.0760.08490.4817-0.1055-0.030.41550.02770.3311-6.03274.6149-12.1871
142.03911.0967-0.00666.1274-0.25232.4738-0.0488-0.08480.07310.13180.04130.034-0.0282-0.03020.01920.10430.02420.0270.1934-0.01880.1298-4.546421.4974-20.547
152.19291.33640.81612.234-0.62021.3177-0.2177-0.42130.69520.17780.4091-0.3209-0.23340.29970.06460.386-0.0353-0.00870.355-0.17680.37516.61435.2789-12.4031
164.1296-4.23571.76319.9667-6.39715.3528-0.8603-0.85930.38041.15810.4682-1.6092-0.5340.06580.20570.36060.0409-0.06890.4012-0.06310.327920.605619.8849-3.9932
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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