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- PDB-8blm: Structure of RutB -

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Basic information

Entry
Database: PDB / ID: 8blm
TitleStructure of RutB
ComponentsUreidoacrylate amidohydrolase RutB
KeywordsHYDROLASE
Function / homologyUreidoacrylate amidohydrolase RutB / ureidoacrylate amidohydrolase / uracil catabolic process / nitrogen utilization / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Ureidoacrylate amidohydrolase RutB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 1.4Nov 15, 2023Group: Source and taxonomy / Category: 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


Theoretical massNumber of molelcules
Total (without water)403,67316
Polymers403,67316
Non-polymers00
Water22,1941232
1
A: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-18 kcal/mol
Surface area15970 Å2
MethodPISA
2
B: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-17 kcal/mol
Surface area16120 Å2
MethodPISA
3
C: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22 kcal/mol
Surface area16000 Å2
MethodPISA
4
D: Ureidoacrylate amidohydrolase RutB

F: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area3650 Å2
ΔGint-20 kcal/mol
Surface area15940 Å2
MethodPISA
5
I: Ureidoacrylate amidohydrolase RutB
O: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-19 kcal/mol
Surface area15900 Å2
MethodPISA
6
J: Ureidoacrylate amidohydrolase RutB

P: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area3660 Å2
ΔGint-17 kcal/mol
Surface area15800 Å2
MethodPISA
7
K: Ureidoacrylate amidohydrolase RutB

M: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area3670 Å2
ΔGint-20 kcal/mol
Surface area15930 Å2
MethodPISA
8
L: Ureidoacrylate amidohydrolase RutB

N: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4592
Polymers50,4592
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 area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.592, 110.890, 128.714
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ureidoacrylate amidohydrolase RutB


Mass: 25229.562 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.05 %
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 300K / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.67 Å / Num. obs: 221505 / % possible obs: 83.44 % / Redundancy: 6.3 % / CC1/2: 0.984 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 714 / CC1/2: 0.196

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.9→47.67 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 44.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.318 21360 5.01 %
Rwork0.2633 --
obs0.266 221197 81.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27284 0 0 1232 28516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828063
X-RAY DIFFRACTIONf_angle_d0.94338285
X-RAY DIFFRACTIONf_dihedral_angle_d6.9613752
X-RAY DIFFRACTIONf_chiral_restr0.0524278
X-RAY DIFFRACTIONf_plane_restr0.0075004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.703520.520543X-RAY DIFFRACTION0
1.92-1.940.812670.556113X-RAY DIFFRACTION1
1.94-1.970.7583300.5329535X-RAY DIFFRACTION3
1.97-1.990.52021000.44671766X-RAY DIFFRACTION11
1.99-2.020.45331970.45373625X-RAY DIFFRACTION22
2.02-2.050.4595930.396511363X-RAY DIFFRACTION69
2.05-2.070.40168650.354516491X-RAY DIFFRACTION99
2.07-2.110.38488670.368416450X-RAY DIFFRACTION99
2.11-2.140.39648790.363616552X-RAY DIFFRACTION99
2.14-2.170.37858710.341116466X-RAY DIFFRACTION99
2.17-2.210.49218270.416715577X-RAY DIFFRACTION94
2.21-2.250.5897320.466113691X-RAY DIFFRACTION82
2.25-2.290.37918630.347716356X-RAY DIFFRACTION99
2.29-2.340.37688670.30316364X-RAY DIFFRACTION99
2.34-2.390.36318680.30616412X-RAY DIFFRACTION99
2.39-2.450.3658570.298816236X-RAY DIFFRACTION98
2.45-2.510.33718570.284816417X-RAY DIFFRACTION99
2.51-2.580.36178710.283416471X-RAY DIFFRACTION99
2.58-2.650.35778650.282216427X-RAY DIFFRACTION99
2.65-2.740.34048510.280416238X-RAY DIFFRACTION98
2.74-2.840.31818660.278416356X-RAY DIFFRACTION98
2.84-2.950.34238520.270916253X-RAY DIFFRACTION98
2.95-3.080.32768540.277516221X-RAY DIFFRACTION98
3.08-3.250.33788600.265916253X-RAY DIFFRACTION98
3.25-3.450.31228450.257716171X-RAY DIFFRACTION97
3.45-3.720.32318380.249415909X-RAY DIFFRACTION96
3.72-4.090.25478360.207915974X-RAY DIFFRACTION96
4.09-4.680.22648360.181115899X-RAY DIFFRACTION95
4.68-5.90.23958560.182216261X-RAY DIFFRACTION98
5.9-47.670.21818480.188216204X-RAY DIFFRACTION98

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