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- PDB-8tg1: Caldicellulosiruptor saccharolyticus periplasmic urea-binding protein -

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Basic information

Entry
Database: PDB / ID: 8tg1
TitleCaldicellulosiruptor saccharolyticus periplasmic urea-binding protein
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / UREA BINDING PROTEIN
Function / homologyUrea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein domain / Leu/Ile/Val-binding protein / amino acid transport / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / BROMIDE ION / UREA / Extracellular ligand-binding receptor
Function and homology information
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsAllert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Becton-Dickinson and Company United States
CitationJournal: To Be Published
Title: Structure-based functional analysis reveals multiple roles and widespread use of urea-binding proteins in nitrogen metabolism
Authors: Allert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular ligand-binding receptor
B: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6835
Polymers87,4832
Non-polymers2003
Water18,2311012
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.235, 91.670, 96.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 43741.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria)
Gene: Csac_2475 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XMB7
#2: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 25% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0162 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0162 Å / Relative weight: 1
ReflectionResolution: 2.097→45.83 Å / Num. obs: 41757 / % possible obs: 99.55 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1671 / Rpim(I) all: 0.09547 / Net I/σ(I): 8.73
Reflection shellResolution: 2.097→2.172 Å / Rmerge(I) obs: 0.7254 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 4073 / CC1/2: 0.809 / Rpim(I) all: 0.4144

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pea

1pea


Resolution: 2.097→45.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 3693 4.75 %
Rwork0.1811 --
obs0.1837 41728 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.097→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 9 1012 6843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.572
X-RAY DIFFRACTIONf_dihedral_angle_d5.344795
X-RAY DIFFRACTIONf_chiral_restr0.045884
X-RAY DIFFRACTIONf_plane_restr0.0041043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.097-2.120.38881490.31552765X-RAY DIFFRACTION96
2.12-2.150.34281090.28362922X-RAY DIFFRACTION98
2.15-2.180.27141600.26782798X-RAY DIFFRACTION98
2.18-2.220.28611570.25112818X-RAY DIFFRACTION97
2.22-2.250.3031210.24152894X-RAY DIFFRACTION97
2.25-2.290.34641550.23842838X-RAY DIFFRACTION98
2.29-2.330.32441250.2332847X-RAY DIFFRACTION98
2.33-2.370.30311480.23162828X-RAY DIFFRACTION98
2.37-2.420.2781410.21882887X-RAY DIFFRACTION98
2.42-2.460.25611360.2192856X-RAY DIFFRACTION98
2.47-2.520.29941500.21372795X-RAY DIFFRACTION97
2.52-2.580.2471340.21962888X-RAY DIFFRACTION98
2.58-2.640.27611500.19782843X-RAY DIFFRACTION98
2.64-2.710.25581400.19042862X-RAY DIFFRACTION98
2.71-2.790.25491420.1912825X-RAY DIFFRACTION98
2.79-2.880.24931320.18382890X-RAY DIFFRACTION98
2.88-2.990.24571560.17622829X-RAY DIFFRACTION98
2.99-3.110.26511330.16022882X-RAY DIFFRACTION98
3.11-3.250.19281360.15522840X-RAY DIFFRACTION98
3.25-3.420.20941520.14462850X-RAY DIFFRACTION98
3.42-3.630.17721430.13512860X-RAY DIFFRACTION98
3.63-3.910.17131370.13172863X-RAY DIFFRACTION98
3.91-4.310.17991450.1272853X-RAY DIFFRACTION97
4.31-4.930.17041420.12492829X-RAY DIFFRACTION97
4.93-6.20.19891520.15692860X-RAY DIFFRACTION99
6.21-45.830.19841480.16682864X-RAY DIFFRACTION98

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