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- PDB-8bkd: structure of RutB -

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Basic information

Entry
Database: PDB / ID: 8bkd
Titlestructure of RutB
ComponentsUreidoacrylate amidohydrolase RutB
KeywordsHYDROLASE
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
N-(AMINOCARBONYL)-BETA-ALANINE / Ureidoacrylate amidohydrolase RutB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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

Downloads & links

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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)407,73124
Polymers406,67416
Non-polymers1,0578
Water88,5084913
1
A: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-21 kcal/mol
Surface area15990 Å2
MethodPISA
2
B: Ureidoacrylate amidohydrolase RutB
D: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area16160 Å2
MethodPISA
3
E: Ureidoacrylate amidohydrolase RutB

O: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,8342
Polymers50,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area3670 Å2
ΔGint-20 kcal/mol
Surface area16290 Å2
MethodPISA
4
F: Ureidoacrylate amidohydrolase RutB
P: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-21 kcal/mol
Surface area16080 Å2
MethodPISA
5
G: Ureidoacrylate amidohydrolase RutB
hetero molecules

I: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area4080 Å2
ΔGint-22 kcal/mol
Surface area16070 Å2
MethodPISA
6
H: Ureidoacrylate amidohydrolase RutB
J: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0994
Polymers50,8342
Non-polymers2642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-23 kcal/mol
Surface area16040 Å2
MethodPISA
7
K: Ureidoacrylate amidohydrolase RutB
M: Ureidoacrylate amidohydrolase RutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-22 kcal/mol
Surface area15960 Å2
MethodPISA
8
L: Ureidoacrylate amidohydrolase RutB
hetero molecules

N: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,9663
Polymers50,8342
Non-polymers1321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area4070 Å2
ΔGint-21 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.920, 111.610, 128.980
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ureidoacrylate amidohydrolase RutB


Mass: 25417.145 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: ATCC 33849 / DSM 4235 / NCIMB 12045 / K12 / DH1 / Gene: rutB, EcDH1_2631, ECDH1ME8569_0965 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QZ65, ureidoacrylate amidohydrolase
#2: Chemical
ChemComp-URP / N-(AMINOCARBONYL)-BETA-ALANINE / N-CARBAMYL-BETA-ALANINE / BETA-UREIDOPROPIONATE


Mass: 132.118 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4913 / 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: 44.58 %
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: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→48.22 Å / Num. obs: 661819 / % possible obs: 98.29 % / Redundancy: 11.1 % / CC1/2: 0.99 / Net I/σ(I): 11.03
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 64589 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.18rc2refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→48.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 2001 0.3 %
Rwork0.1687 --
obs0.1688 661493 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27547 0 72 4913 32532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00528331
X-RAY DIFFRACTIONf_angle_d0.79238635
X-RAY DIFFRACTIONf_dihedral_angle_d8.1123801
X-RAY DIFFRACTIONf_chiral_restr0.0764312
X-RAY DIFFRACTIONf_plane_restr0.0065056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.34241510.301445777X-RAY DIFFRACTION96
1.43-1.470.34191120.277346302X-RAY DIFFRACTION97
1.47-1.520.3111520.257646513X-RAY DIFFRACTION97
1.52-1.570.28121550.222846556X-RAY DIFFRACTION97
1.57-1.620.25481380.192146725X-RAY DIFFRACTION98
1.62-1.690.23511390.17646891X-RAY DIFFRACTION98
1.69-1.760.25381370.170547008X-RAY DIFFRACTION98
1.76-1.860.21131420.162747156X-RAY DIFFRACTION98
1.86-1.970.22371470.159547300X-RAY DIFFRACTION99
1.97-2.130.18961430.151747469X-RAY DIFFRACTION99
2.13-2.340.19251530.154147597X-RAY DIFFRACTION99
2.34-2.680.21241400.161247784X-RAY DIFFRACTION100
2.68-3.370.19551450.161347974X-RAY DIFFRACTION100
3.37-48.220.18141470.150548440X-RAY DIFFRACTION100

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