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- PDB-7s6e: Crystal structure of UrtA from Synechococcus CC9311 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7s6e
TitleCrystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium
ComponentsUrea ABC transporter, periplasmic urea-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / urea-binding protein
Function / homology
Function and homology information


Urea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UREA / Urea ABC transporter, periplasmic urea-binding protein
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 Å
AuthorsShah, B.S. / Mikolajek, H. / Mykhaylyk, V. / Orr, C.M. / Owens, R.J. / Paulsen, I.T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102944 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium
Authors: Shah, B.S. / Mikolajek, H. / Mykhaylyk, V. / Orr, C.M. / Owens, R. / Paulsen, I.T.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urea ABC transporter, periplasmic urea-binding protein
B: Urea ABC transporter, periplasmic urea-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,70427
Polymers88,4472
Non-polymers1,25725
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-107 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.760, 117.120, 123.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Urea ABC transporter, periplasmic urea-binding protein


Mass: 44223.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria)
Strain: CC9311 / Gene: sync_2872 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q0I663

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Non-polymers , 5 types, 662 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.062 M MES; 0.038 imidazole, pH 6.5, 0.03M MgCl2, 0.03M CaCl2.2H2O, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.0240, 3.3509, 4.2753, 4.7686
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 26, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
13.0241
23.35091
34.27531
44.76861
ReflectionResolution: 1.97→85.114 Å / Num. obs: 49942 / % possible obs: 93.3 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.026 / Rrim(I) all: 0.08 / Net I/σ(I): 22.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.04-84.97220.0426300.9990.0120.043
1.97-2.026.70.29525500.9450.1720.343

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Cootmodel building
CRANK2phasing
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.973→85.114 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.146 / SU B: 2.842 / SU ML: 0.08 / Average fsc free: 0.9627 / Average fsc work: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1737 2526 5.058 %
Rwork0.1467 47416 -
all0.148 --
obs-49942 96.577 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.669 Å20 Å20 Å2
2--0.378 Å2-0 Å2
3----1.047 Å2
Refinement stepCycle: LAST / Resolution: 1.973→85.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 61 637 6915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175903
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6498699
X-RAY DIFFRACTIONr_angle_other_deg1.4151.58113719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86925.133300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.858151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6481512
X-RAY DIFFRACTIONr_chiral_restr0.090.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021359
X-RAY DIFFRACTIONr_nbd_refined0.2070.21264
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25634
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23087
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22666
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2541
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.237
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.222
X-RAY DIFFRACTIONr_nbd_other0.2740.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1340.24
X-RAY DIFFRACTIONr_mcbond_it1.8622.1893198
X-RAY DIFFRACTIONr_mcbond_other1.8572.1883196
X-RAY DIFFRACTIONr_mcangle_it2.3653.2683995
X-RAY DIFFRACTIONr_mcangle_other2.3653.2683996
X-RAY DIFFRACTIONr_scbond_it2.7962.4533225
X-RAY DIFFRACTIONr_scbond_other2.7952.4543226
X-RAY DIFFRACTIONr_scangle_it4.0773.5564704
X-RAY DIFFRACTIONr_scangle_other4.0773.5574705
X-RAY DIFFRACTIONr_lrange_it5.0326.3437412
X-RAY DIFFRACTIONr_lrange_other5.02526.3417410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.973-2.0240.221420.173072X-RAY DIFFRACTION84.9815
2.024-2.080.1891580.1623291X-RAY DIFFRACTION93.6211
2.08-2.140.1821900.1553178X-RAY DIFFRACTION94.6865
2.14-2.2060.1821740.1433119X-RAY DIFFRACTION94.8445
2.206-2.2780.2051680.1433043X-RAY DIFFRACTION95.0281
2.278-2.3580.2061650.1422973X-RAY DIFFRACTION96.1103
2.358-2.4470.1841580.1482901X-RAY DIFFRACTION97.4825
2.447-2.5470.1851690.1452800X-RAY DIFFRACTION97.2805
2.547-2.660.1841600.1382690X-RAY DIFFRACTION97.6696
2.66-2.790.1871230.1442636X-RAY DIFFRACTION98.4654
2.79-2.9410.161190.1462549X-RAY DIFFRACTION99.478
2.941-3.1190.1821270.1492385X-RAY DIFFRACTION100
3.119-3.3340.1731150.1622277X-RAY DIFFRACTION100
3.334-3.6010.164930.1562124X-RAY DIFFRACTION100
3.601-3.9450.192950.1391961X-RAY DIFFRACTION100
3.945-4.410.151920.1211794X-RAY DIFFRACTION99.947
4.41-5.0910.156830.1311582X-RAY DIFFRACTION100
5.091-6.2320.172730.161354X-RAY DIFFRACTION100
6.232-8.8030.144850.1621045X-RAY DIFFRACTION100

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