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- PDB-6ulo: Structure of an N-terminally truncated uncharacterized protein fr... -

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Basic information

Entry
Database: PDB / ID: 6ulo
TitleStructure of an N-terminally truncated uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologymembrane => GO:0016020 / Uncharacterized protein
Function and homology information
Biological speciesLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of an N-terminally truncated uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1484
Polymers76,0772
Non-polymers712
Water18,3931021
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0742
Polymers38,0381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0742
Polymers38,0381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.440, 56.650, 60.990
Angle α, β, γ (deg.)98.637, 106.327, 83.326
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Uncharacterized protein


Mass: 38038.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria)
Strain: Fiocruz L1-130 / Gene: LIC_10985 / Plasmid: LpinA.19565.a.B2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q72TN2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Molecular Dimensions Morpheus screen, condition H5: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each amino acid: sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM ...Details: Molecular Dimensions Morpheus screen, condition H5: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each amino acid: sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MOPS/HEPES-Na pH 7.5: LpinA.195645.a.B2.PW386228 at 23mg/ml. Cryo: direct: tray 310523 h5: puck PAS1-8. For phasing a crystal from the same tray, well C1 (10% w/v PEG 20 000, 20% v/v PEG MME 550: 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5) was incubated for 20sec in a mixture of 10% 5M sodium iodide in ethylene glycol (500mM final NaI concentration) and 90% reservoir solution. Diffraction data were collected in-house.Tray 310523 c1: puck LOF7-9

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDAug 15, 2019
RIGAKU SATURN 944+2CCDSep 20, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C(111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.3→50 Å / Num. obs: 155840 / % possible obs: 95.3 % / Redundancy: 3.927 % / Biso Wilson estimate: 19.615 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.041 / Χ2: 1.052 / Net I/σ(I): 19.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.333.9530.5572.35111650.8350.64592.6
1.33-1.373.9510.4462.94109890.8860.51692.9
1.37-1.413.9470.3743.56106560.9180.43393.2
1.41-1.453.9440.2984.48105120.9440.34493.6
1.45-1.53.9460.2245.9101090.9670.25994.1
1.5-1.553.940.177.7498080.9780.19694.3
1.55-1.613.9290.1369.6495250.9860.15794.9
1.61-1.683.9320.1111.8392440.990.12895.2
1.68-1.753.9380.08714.6589150.9930.10195.4
1.75-1.843.9420.06818.7984840.9950.07895.9
1.84-1.943.9340.05223.5681740.9970.0696.4
1.94-2.063.9320.0429.8276940.9980.04796.6
2.06-2.23.9110.03236.0673310.9990.03797.1
2.2-2.373.9060.02839.9867880.9990.03397.3
2.37-2.63.8920.02643.3462740.9990.0397.8
2.6-2.913.860.02446.4957310.9990.02898.1
2.91-3.363.8680.0251.2350280.9990.02398.7
3.36-4.113.8810.01855.5142930.9990.0298.8
4.11-5.813.9070.01756.4933180.9990.01999.1
5.81-503.8160.01856.4218020.9990.02198.5

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PARROTphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→32.24 Å / SU ML: 0.1214 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.6941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 1916 1.23 %0
Rwork0.1375 153900 --
obs0.138 155816 95.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.46 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 2 1021 5949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935257
X-RAY DIFFRACTIONf_angle_d1.11227169
X-RAY DIFFRACTIONf_chiral_restr0.0849815
X-RAY DIFFRACTIONf_plane_restr0.0071914
X-RAY DIFFRACTIONf_dihedral_angle_d14.33642041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.24021340.215610632X-RAY DIFFRACTION92.48
1.33-1.370.22191340.19110707X-RAY DIFFRACTION92.9
1.37-1.410.1991250.175910768X-RAY DIFFRACTION93.21
1.41-1.450.21351320.157310882X-RAY DIFFRACTION93.78
1.45-1.510.20931270.143510757X-RAY DIFFRACTION94.1
1.51-1.570.17781220.131410934X-RAY DIFFRACTION94.4
1.57-1.640.17291310.128110929X-RAY DIFFRACTION95.06
1.64-1.720.15551520.1310964X-RAY DIFFRACTION95.42
1.72-1.830.17021520.128211041X-RAY DIFFRACTION95.92
1.83-1.970.18221550.135211131X-RAY DIFFRACTION96.4
1.97-2.170.17581340.128311198X-RAY DIFFRACTION97
2.17-2.490.15741370.133811214X-RAY DIFFRACTION97.53
2.49-3.130.17081490.140811325X-RAY DIFFRACTION98.25
3.13-32.240.15871320.130611418X-RAY DIFFRACTION99.01

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