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- PDB-5bos: Structure of Acetobacter aceti PurE-S57C, partly oxidized form -

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Basic information

Entry
Database: PDB / ID: 5bos
TitleStructure of Acetobacter aceti PurE-S57C, partly oxidized form
Components(N5-carboxyaminoimidazole ribonucleotide ...) x 2
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: 1.712 Å
AuthorsSullivan, K.L. / Kappock, T.J.
CitationJournal: To Be Published
Title: Mutation of the conserved serine in two PurE classes
Authors: Sullivan, K.L. / Kappock, T.J.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)38,2358
Polymers37,8622
Non-polymers3746
Water7,620423
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)152,94132
Polymers151,4468
Non-polymers1,49524
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 area35060 Å2
ΔGint-140 kcal/mol
Surface area38570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.584, 99.584, 164.702
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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N5-carboxyaminoimidazole ribonucleotide ... , 2 types, 2 molecules AB

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


Mass: 18946.773 Da / Num. of mol.: 1 / Mutation: S57C
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(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Protein N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase


Mass: 18914.777 Da / Num. of mol.: 1 / Mutation: S57C
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(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

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Non-polymers , 5 types, 429 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 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: Nov 15, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.712→50 Å / Num. obs: 44754 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.2 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.075 / Net I/σ(I): 81.8
Reflection shellResolution: 1.712→1.75 Å / Redundancy: 24.4 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 11.4 / % possible all: 100

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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 chain A

4ycb


Resolution: 1.712→42.609 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 2129 4.76 %Same as 4z7j
Rwork0.1346 ---
obs0.1358 44701 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.712→42.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 22 423 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072565
X-RAY DIFFRACTIONf_angle_d1.0493536
X-RAY DIFFRACTIONf_dihedral_angle_d12.255956
X-RAY DIFFRACTIONf_chiral_restr0.044422
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7121-1.75190.181360.14692729X-RAY DIFFRACTION98
1.7519-1.79570.15551410.14382812X-RAY DIFFRACTION100
1.7957-1.84430.1681400.15392802X-RAY DIFFRACTION100
1.8443-1.89850.18011400.14782798X-RAY DIFFRACTION100
1.8985-1.95980.16091400.14022807X-RAY DIFFRACTION100
1.9598-2.02990.16641410.14122811X-RAY DIFFRACTION100
2.0299-2.11110.17651410.13712822X-RAY DIFFRACTION100
2.1111-2.20720.16711410.13512827X-RAY DIFFRACTION100
2.2072-2.32360.16081410.13472820X-RAY DIFFRACTION100
2.3236-2.46910.16891420.13622838X-RAY DIFFRACTION100
2.4691-2.65970.17971410.14042833X-RAY DIFFRACTION100
2.6597-2.92730.18411440.1462866X-RAY DIFFRACTION100
2.9273-3.35080.15431420.13542865X-RAY DIFFRACTION100
3.3508-4.22110.13161460.11942903X-RAY DIFFRACTION100
4.2211-42.62220.15591530.1263039X-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)
12.269-1.944-0.19212.3038-1.84096.32040.0693-0.33020.48370.23950.03230.205-0.2514-0.07010.01650.09260.0176-0.01130.1167-0.05730.1775-5.988830.283235.7214
25.73985.8491-0.11729.2686-0.71194.43030.134-0.5488-0.05330.2844-0.2107-0.08020.1744-0.00540.0480.11940.0217-0.00210.1723-0.02310.0938-0.844123.038541.0604
37.34535.25163.21924.86192.27931.98330.1594-0.2810.08020.2462-0.1654-0.03280.088-0.14550.02910.13060.00080.00820.1261-0.04540.1108-8.448327.287836.0178
48.44816.7023-2.92715.6334-2.38021.7853-0.08930.16730.5733-0.04760.10070.416-0.0535-0.1427-0.02960.12370.0342-0.01920.1209-0.03070.1943-16.577130.546828.3051
52.3383-0.32430.55725.0149-0.02391.5759-0.0337-0.04090.2172-0.0558-0.08830.0982-0.0533-0.09620.08850.07340.0030.00270.0937-0.01830.0906-7.707426.767927.0005
61.09760.3554-2.30497.43310.62885.09990.2592-0.5729-0.48510.9507-0.2389-0.40950.3677-0.11540.06640.239-0.0563-0.03610.23210.0560.1949-4.47685.872534.5184
71.89761.34680.35472.94460.17831.1403-0.03730.04770.0589-0.03740.010.013-0.06250.01130.0320.07390.01330.00170.1016-0.00670.08180.620621.827925.9339
84.9636-4.32733.43364.4225-3.24743.11990.03030.14160.0452-0.0214-0.0758-0.0782-0.04120.14260.0370.1164-0.0192-0.02670.1211-0.04030.133815.07932.195135.2148
94.1906-5.78252.1719.5038-5.31346.0282-0.0712-0.4363-0.28481.04670.3307-0.28270.42250.0833-0.11090.34110.0264-0.09250.1751-0.02470.203324.364114.509943.2291
104.3930.52990.85770.21710.91294.43860.15670.26840.2334-0.3055-0.0998-0.1344-0.06910.0998-0.00230.1691-0.0290.01740.13630.04240.095913.645227.494211.3303
114.5445-3.6794-2.23718.13693.9142.73270.07640.44660.0247-0.3306-0.21010.1987-0.0566-0.11890.1250.2019-0.02-0.02350.20290.0290.08086.888322.36676.0181
121.7392-0.35870.12411.3881-0.26221.0190.00860.10380.17-0.1262-0.0509-0.1739-0.07710.11680.05640.1324-0.0187-0.00310.10420.02080.112716.586624.616817.713
133.9173.43980.26453.02460.37916.4793-0.02120.575-0.3802-0.76660.15950.37490.66430.06640.0330.24170.0227-0.03130.2048-0.03740.17225.85694.707212.1627
141.2807-0.6161-0.02583.92340.22241.2161-0.03840.01040.0581-0.06080.03220.0155-0.04560.01550.01860.0629-0.01250.00450.09950.00610.07064.827221.557420.9369
156.80525.66772.57775.82672.65061.4888-0.1807-0.01020.4648-0.10660.13540.4672-0.1907-0.26060.0770.26320.0231-0.06360.22540.09850.265-6.641135.458112.2088
164.85184.51342.40855.46052.78521.4314-0.44190.4415-0.0078-1.09330.40630.9108-0.2154-0.00510.12750.3854-0.0447-0.09660.38870.0610.3077-21.076319.15622.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:30 )A20 - 30
2X-RAY DIFFRACTION2( CHAIN A AND RESID 31:46 )A31 - 46
3X-RAY DIFFRACTION3( CHAIN A AND RESID 47:61 )A47 - 61
4X-RAY DIFFRACTION4( CHAIN A AND RESID 62:72 )A62 - 72
5X-RAY DIFFRACTION5( CHAIN A AND RESID 73:107 )A73 - 107
6X-RAY DIFFRACTION6( CHAIN A AND RESID 108:114 )A108 - 114
7X-RAY DIFFRACTION7( CHAIN A AND RESID 115:154 )A115 - 154
8X-RAY DIFFRACTION8( CHAIN A AND RESID 155:171 )A155 - 171
9X-RAY DIFFRACTION9( CHAIN A AND RESID 172:179 )A172 - 179
10X-RAY DIFFRACTION10( CHAIN B AND RESID 20:30 )B20 - 30
11X-RAY DIFFRACTION11( CHAIN B AND RESID 31:46 )B31 - 46
12X-RAY DIFFRACTION12( CHAIN B AND RESID 47:107 )B47 - 107
13X-RAY DIFFRACTION13( CHAIN B AND RESID 108:114 )B108 - 114
14X-RAY DIFFRACTION14( CHAIN B AND RESID 115:154 )B115 - 154
15X-RAY DIFFRACTION15( CHAIN B AND RESID 155:171 )B155 - 171
16X-RAY DIFFRACTION16( CHAIN B AND RESID 172:180 )B172 - 180

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