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- PDB-8bll: Structure of RutB -

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Basic information

Entry
Database: PDB / ID: 8bll
TitleStructure of RutB
ComponentsUreidoacrylate amidohydrolase RutB
KeywordsHYDROLASE / amidohydrolase
Function / homology
Function and homology information


ureidoacrylate amidohydrolase / uracil catabolic process / nitrogen utilization / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function
Ureidoacrylate amidohydrolase RutB / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family
Similarity search - Domain/homology
ACETATE ION / Ureidoacrylate amidohydrolase RutB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRajendran, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli .
Authors: Busch, M.R. / Rajendran, C. / Sterner, R.
History
DepositionNov 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ureidoacrylate amidohydrolase RutB
B: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB
D: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB
F: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB
I: Ureidoacrylate amidohydrolase RutB
J: Ureidoacrylate amidohydrolase RutB
K: Ureidoacrylate amidohydrolase RutB
L: Ureidoacrylate amidohydrolase RutB
M: Ureidoacrylate amidohydrolase RutB
N: Ureidoacrylate amidohydrolase RutB
O: Ureidoacrylate amidohydrolase RutB
P: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,30548
Polymers403,41616
Non-polymers1,88932
Water59,7023314
1
A: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-26 kcal/mol
Surface area15980 Å2
MethodPISA
2
B: Ureidoacrylate amidohydrolase RutB
F: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-25 kcal/mol
Surface area15960 Å2
MethodPISA
3
D: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-25 kcal/mol
Surface area15780 Å2
MethodPISA
4
G: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area15850 Å2
MethodPISA
5
I: Ureidoacrylate amidohydrolase RutB
hetero molecules

K: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4660 Å2
ΔGint-25 kcal/mol
Surface area16010 Å2
MethodPISA
6
J: Ureidoacrylate amidohydrolase RutB
hetero molecules

O: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area4650 Å2
ΔGint-25 kcal/mol
Surface area15860 Å2
MethodPISA
7
L: Ureidoacrylate amidohydrolase RutB
hetero molecules

M: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4660 Å2
ΔGint-25 kcal/mol
Surface area15910 Å2
MethodPISA
8
N: Ureidoacrylate amidohydrolase RutB
hetero molecules

P: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6636
Polymers50,4272
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4670 Å2
ΔGint-27 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.456, 108.609, 124.341
Angle α, β, γ (deg.)85.66, 83.22, 74.34
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Ureidoacrylate amidohydrolase RutB


Mass: 25213.498 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: rutB, EcDH1_2631, ECDH1ME8569_0965 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QZ65, ureidoacrylate amidohydrolase
#2: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→47 Å / Num. obs: 472783 / % possible obs: 87.81 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.45 Å2 / CC1/2: 0.974 / Net I/σ(I): 7.2
Reflection shellResolution: 1.54→1.59 Å / Num. unique obs: 47452 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→47 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 42915 5 %
Rwork0.2072 --
obs0.209 472783 83.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27420 0 128 3314 30862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01228244
X-RAY DIFFRACTIONf_angle_d1.12238498
X-RAY DIFFRACTIONf_dihedral_angle_d6.1523758
X-RAY DIFFRACTIONf_chiral_restr0.0584288
X-RAY DIFFRACTIONf_plane_restr0.0085054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.370614330.346727100X-RAY DIFFRACTION84
1.56-1.580.348615420.324329411X-RAY DIFFRACTION90
1.58-1.60.326915480.320429597X-RAY DIFFRACTION91
1.6-1.620.347415830.318729953X-RAY DIFFRACTION92
1.62-1.640.346515670.31429794X-RAY DIFFRACTION92
1.64-1.660.314515820.294930126X-RAY DIFFRACTION93
1.66-1.680.316715780.280230099X-RAY DIFFRACTION93
1.68-1.710.317715940.274530228X-RAY DIFFRACTION93
1.71-1.740.310715950.270830417X-RAY DIFFRACTION93
1.74-1.760.30415960.269830241X-RAY DIFFRACTION93
1.76-1.790.29115940.247530321X-RAY DIFFRACTION94
1.79-1.830.26916120.225730618X-RAY DIFFRACTION94
1.83-1.860.329314770.280628027X-RAY DIFFRACTION87
1.86-1.90.65717110.565813378X-RAY DIFFRACTION41
1.9-1.940.68622070.6043959X-RAY DIFFRACTION12
1.94-1.990.472510340.427519738X-RAY DIFFRACTION61
1.99-2.040.246615800.203930172X-RAY DIFFRACTION93
2.04-2.090.2316080.189330760X-RAY DIFFRACTION95
2.09-2.150.225616170.183630824X-RAY DIFFRACTION95
2.15-2.220.374812150.347823011X-RAY DIFFRACTION71
2.22-2.30.62984990.50829540X-RAY DIFFRACTION29
2.3-2.390.221515400.175429208X-RAY DIFFRACTION90
2.39-2.50.204216140.159730788X-RAY DIFFRACTION95
2.5-2.630.196416270.153930902X-RAY DIFFRACTION95
2.63-2.80.19816290.157631029X-RAY DIFFRACTION95
2.8-3.020.20816230.15730991X-RAY DIFFRACTION95
3.02-3.320.202616290.173230815X-RAY DIFFRACTION95
3.32-3.80.260812910.224124269X-RAY DIFFRACTION75
3.8-4.790.149715180.128528884X-RAY DIFFRACTION89
4.79-470.176416720.151831558X-RAY DIFFRACTION97

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