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

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Basic information

Entry
Database: PDB / ID: 4ycd
TitleStructure of a single tryptophan mutant of Acetobacter aceti PurE with Y154F
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 / MOLECULAR REPLACEMENT / Resolution: 1.643 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 1.1Sep 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: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,33711
Polymers37,5772
Non-polymers7609
Water8,089449
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)153,34744
Polymers150,3098
Non-polymers3,03836
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 area37910 Å2
ΔGint-412 kcal/mol
Surface area37630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.336, 100.336, 165.712
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-374-

HOH

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Components

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


Mass: 18788.639 Da / Num. of mol.: 2 / Mutation: W34F, Y154F, 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 (E. coli) / Strain (production host): BL21
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 25% (v/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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.628→48.389 Å / Num. obs: 51530 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 12.68 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.087 / Net I/σ(I): 26.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCB

4ycb


Resolution: 1.643→48.389 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 2032 3.94 %same as 4YCB
Rwork0.137 ---
obs0.1379 51521 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.643→48.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 42 449 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092546
X-RAY DIFFRACTIONf_angle_d1.233516
X-RAY DIFFRACTIONf_dihedral_angle_d11.994963
X-RAY DIFFRACTIONf_chiral_restr0.048422
X-RAY DIFFRACTIONf_plane_restr0.007462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6428-1.6810.2141270.17083085X-RAY DIFFRACTION95
1.681-1.72310.19651340.17023264X-RAY DIFFRACTION100
1.7231-1.76970.1771330.15813267X-RAY DIFFRACTION100
1.7697-1.82180.17351230.15193292X-RAY DIFFRACTION100
1.8218-1.88060.157340.14373404X-RAY DIFFRACTION100
1.8806-1.94780.114420.15113411X-RAY DIFFRACTION100
1.9478-2.02580.15761210.15123278X-RAY DIFFRACTION100
2.0258-2.1180.16311850.13553225X-RAY DIFFRACTION100
2.118-2.22960.15851700.13793274X-RAY DIFFRACTION100
2.2296-2.36930.1591780.13533261X-RAY DIFFRACTION100
2.3693-2.55220.17121740.1383251X-RAY DIFFRACTION100
2.5522-2.80910.17431700.14243297X-RAY DIFFRACTION100
2.8091-3.21550.16351780.14093310X-RAY DIFFRACTION100
3.2155-4.05080.13131700.1183351X-RAY DIFFRACTION100
4.0508-48.41010.13761630.12183519X-RAY DIFFRACTION100
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)
12.14140.05950.32862.5669-1.03711.78250.13980.2305-0.2883-0.1266-0.09680.19170.11360.01580.08350.11360.0084-0.00520.1055-0.03210.1321-5.4559-30.2963-35.9946
23.3256-1.7634-0.00612.83990.00490.90710.02860.36870.0178-0.1543-0.0918-0.0834-0.0611-0.01660.01130.14380.00510.00570.1641-0.01630.1025-0.0935-23.2934-41.3946
32.7551-0.8572-0.32080.96680.21910.51690.08320.2027-0.1888-0.1944-0.08150.013-0.06-0.0360.01890.11580.0070.0040.1123-0.03070.1152-7.6834-27.7751-36.4537
42.1778-1.36230.92562.5107-0.69440.74930.0068-0.0579-0.32680.0702-0.03670.1280.0333-0.0525-0.00080.1145-0.02260.01240.1279-0.01570.1649-16.0549-30.841-28.615
51.4384-0.2722-0.07491.48220.18580.9112-0.0081-0.0189-0.16390.0796-0.04830.09470.0781-0.07310.02220.0999-0.00270.010.0869-0.00310.1209-7.1325-27.2592-27.3788
65.10940.50950.54886.81590.99211.12040.10830.54030.4449-0.5916-0.1631-0.0608-0.2726-0.12660.13390.20380.050.02270.19620.06940.1594-4.487-5.8571-35.0104
71.1354-0.46110.00271.06620.05720.7378-0.01970.0053-0.04730.0127-0.01760.03060.0236-0.02520.01340.0802-0.0060.00740.0731-0.00250.08141.0876-21.5448-26.4824
82.13811.5843-0.74172.8548-0.76090.71730.0628-0.0438-0.16550.1002-0.0357-0.10290.03590.04880.02360.12520.01320.02730.1098-0.0270.137415.4006-32.3625-35.2382
94.01852.0338-0.71096.803-0.75382.13290.00010.39170.3411-0.54660.025-0.1742-0.3060.0041-0.01610.2545-0.01480.05410.18780.00620.175624.5424-14.0619-43.6567
102.2111-0.2339-0.061.26160.80441.46720.0606-0.1616-0.2230.3132-0.0549-0.10630.13940.07640.04240.17150.0133-0.01250.10880.04210.126413.9537-27.6981-11.8211
112.14931.41240.16113.83250.34680.90140.0224-0.3512-0.02360.4125-0.1120.06970.0181-0.14060.01580.23740.0098-0.00760.17390.02440.09787.2341-22.0776-6.4112
121.32050.14580.13530.9641-0.08550.59650.0132-0.0648-0.10920.0828-0.0471-0.10640.04510.0970.00970.11310.0128-0.00270.08540.01810.098516.9098-24.3321-17.836
136.9085-0.7825-0.51356.548-0.17131.45330.0304-0.5570.3920.8139-0.22550.1492-0.28310.02040.07870.2588-0.030.02540.1788-0.04470.16666.1089-4.3724-12.4977
140.8860.17470.02751.21830.1870.7808-0.0108-0.054-0.04480.0817-0.0146-0.01230.02090.05450.01140.08770.00770.00390.08410.00510.08284.9968-20.9998-20.9178
153.1377-1.9296-0.70232.11770.41820.5523-0.0578-0.1652-0.3491-0.02540.10930.22840.1008-0.07870.04160.2101-0.0090.04310.16060.06220.2008-6.1529-35.2242-12.7912
164.4585-1.2057-0.11162.98580.54973.0905-0.1583-0.2976-0.09120.42310.05990.4974-0.0449-0.18020.0720.25540.02430.03370.25930.0530.1606-19.9511-20.6624-4.3116
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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