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- PDB-5ctj: Structure of a single tryptophan mutant of Acetobacter aceti PurE... -

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Basic information

Entry
Database: PDB / ID: 5ctj
TitleStructure of a single tryptophan mutant of Acetobacter aceti PurE containing 5-fluorotryptophan
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
N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesAcetobacter aceti 1023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.928 Å
AuthorsSullivan, K.L. / Kappock, T.J.
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
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag

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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)38,0557
Polymers37,6452
Non-polymers4105
Water3,333185
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)152,22028
Polymers150,5818
Non-polymers1,63920
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 area35600 Å2
ΔGint-378 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.764, 98.764, 165.070
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-303-

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: 18822.631 Da / Num. of mol.: 2 / Mutation: W34F,W165F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Details (production host): pJK698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 31% PEG 4000, 200 mM lithium sulfate, 100 mM Tris-HCl

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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: Jul 12, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.928→50 Å / Num. all: 31074 / Num. obs: 31081 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 27.04 Å2 / Rsym value: 0.067 / Net I/σ(I): 48.56
Reflection shellResolution: 1.928→1.96 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 5.21 / % possible all: 95.4

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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

4ycb


Resolution: 1.928→42.668 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 1509 4.86 %Same as 4ycb
Rwork0.1412 ---
obs0.1425 31074 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.928→42.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 23 185 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112462
X-RAY DIFFRACTIONf_angle_d1.0063373
X-RAY DIFFRACTIONf_dihedral_angle_d12.638908
X-RAY DIFFRACTIONf_chiral_restr0.046407
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9283-1.99060.2253930.16542623X-RAY DIFFRACTION98
1.9906-2.06170.18371510.15452634X-RAY DIFFRACTION100
2.0617-2.14420.17561330.14212660X-RAY DIFFRACTION100
2.1442-2.24180.16711700.13562636X-RAY DIFFRACTION100
2.2418-2.360.18081290.1412666X-RAY DIFFRACTION100
2.36-2.50790.21611440.14622644X-RAY DIFFRACTION100
2.5079-2.70150.18591280.1452689X-RAY DIFFRACTION100
2.7015-2.97330.18651510.14672671X-RAY DIFFRACTION100
2.9733-3.40330.17361390.14232724X-RAY DIFFRACTION100
3.4033-4.28720.13851360.12882732X-RAY DIFFRACTION100
4.2872-42.6780.15581350.14152886X-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)
15.38092.0707-0.8295.1709-5.15245.46540.1041-0.25770.50680.49890.09850.6052-0.0011-0.1658-0.18050.25910.0166-0.00210.2553-0.07370.283-6.219828.959535.1755
29.16495.88242.03635.11941.54056.48450.1766-0.74640.25720.4962-0.21090.21060.2861-0.1694-0.02750.31030.0339-0.01770.3088-0.05180.2288-0.843422.918640.9624
37.40064.1692.16824.83431.45081.3365-0.0457-0.47240.0370.1174-0.0592-0.1363-0.0352-0.16260.08350.2554-0.0025-0.0010.2522-0.07580.2402-7.96327.590736.0883
48.46937.726-3.41688.388-2.7382.27930.12660.05690.87240.265-0.13210.604-0.279-0.0256-0.03830.25440.0562-0.00220.2315-0.06070.3242-16.441330.227928.6521
53.3412-0.91180.81973.7854-1.02663.4845-0.00580.04220.2297-0.0983-0.04030.0541-0.0224-0.05020.03740.16260.0077-0.00620.1585-0.0250.1664-7.522226.484626.8167
62.0639-1.1193-2.1213.7946-1.23783.97180.554-1.0255-1.12431.6995-0.5084-1.28040.2927-0.18720.30250.4858-0.1169-0.07990.46940.07570.3655-4.53675.796234.5345
72.38181.60430.44735.06270.23022.3786-0.0769-0.00670.15560.06760.01870.1099-0.1330.03670.06850.15640.0156-0.00890.2063-0.02530.18021.14322.270326.4354
87.6167-5.60154.5645.0785-2.93894.58060.0390.01170.0461-0.0606-0.02530.0122-0.03770.2657-0.00880.266-0.0392-0.04370.2647-0.04480.270915.187331.863634.8746
99.337-6.78376.57224.9917-4.8424.801-0.1241-0.2839-0.29811.52360.3776-0.20780.5489-0.2086-0.24680.55770.0128-0.07970.4096-0.0870.304324.438914.848542.5993
107.1386-1.7374-1.31481.62063.01456.29290.04460.26560.3761-0.4188-0.05530.1239-0.23550.11610.0470.2823-0.0323-0.04310.2790.0480.169913.385228.074611.5547
115.6201-3.8899-2.45674.0982.56572.31980.130.4482-0.0712-0.6432-0.0823-0.00020.0632-0.2377-0.04230.3407-0.0538-0.04890.33940.03940.18786.898722.19675.9401
122.83630.02880.10971.0655-0.34691.83360.00330.04360.194-0.0972-0.0352-0.2121-0.09690.1810.02690.2404-0.0343-0.02110.20580.01720.21316.253624.597317.6326
130.480.03791.83582.7207-2.35949.33070.29081.0126-0.7991-1.7329-0.23060.8160.57250.10060.00990.44410.0662-0.0420.4016-0.03890.37456.07114.902112.1085
142.3181-0.99720.39945.77070.12382.5562-0.04620.04770.0931-0.13740.0263-0.0291-0.0810.03780.02980.133-0.01970.00810.19710.01720.15534.410921.693420.3349
154.44635.96792.64528.01373.61342.0386-0.03090.06790.4796-0.0211-0.01920.3399-0.201-0.26810.05680.38850.0424-0.07140.32140.08920.4176-7.011335.321112.2824
164.90185.20864.59165.57344.85034.3852-0.33890.598-0.4137-0.69330.45880.1055-0.37580.0547-0.08550.3915-0.0328-0.02670.44020.00570.3782-20.693618.62082.6538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 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 182 )

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