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- PDB-6osx: Crystal structure of uncharacterized protein ECL_02694 -

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Basic information

Entry
Database: PDB / ID: 6osx
TitleCrystal structure of uncharacterized protein ECL_02694
ComponentsProtein YmbA
KeywordsUNKNOWN FUNCTION / CSGID / structural genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / ACETATE ION / DI(HYDROXYETHYL)ETHER / Membrane integrity-associated transporter subunit PqiC
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.45 Å
AuthorsChang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of uncharacterized protein ECL_02694
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein YmbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8984
Polymers18,6371
Non-polymers2613
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.219, 61.219, 84.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein YmbA / A0A0H3CK21


Mass: 18636.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ymbA, NCTC10005_05664 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M7FD65
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.8M Lithium sulfate, 0.1M Sodium Acetate, 4% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 26979 / % possible obs: 84.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.26 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 0.866 / Net I/σ(I): 11.6 / Num. measured all: 114305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.481.80.3425300.7560.2730.441.03133
1.48-1.51.90.2495730.8870.1960.3190.86636.8
1.5-1.5320.2286910.9050.1760.2890.93643.4
1.53-1.5620.2258200.9150.1690.2830.92350.8
1.56-1.62.20.2139770.9080.1530.2640.96562
1.6-1.632.60.22412350.9350.1440.2680.86676.6
1.63-1.673.10.24614370.9080.1480.2890.89991.1
1.67-1.723.70.24315450.9320.1380.2810.9397.4
1.72-1.774.30.2315950.9420.1230.2620.93999.5
1.77-1.834.50.18515780.9680.0960.2090.99299.4
1.83-1.894.40.1515910.9770.0790.1710.9599.1
1.89-1.9750.11215970.9860.0550.1250.9299.9
1.97-2.0650.08915850.9910.0440.0990.94199.9
2.06-2.175.10.07215840.9940.0350.080.88999.5
2.17-2.350.05915910.9930.0290.0660.8199.8
2.3-2.484.90.05415980.9940.0270.060.80499.4
2.48-2.735.30.04716030.9960.0220.0530.713100
2.73-3.125.20.04216010.9960.020.0460.75499.7
3.12-3.944.90.03815990.9960.0190.0430.82499.6
3.94-5050.03816490.9960.0190.0430.81699.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MIRAS
Starting model: SAD data set

Resolution: 1.45→44.915 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 1351 5.19 %
Rwork0.1451 24661 -
obs0.1469 26012 81.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.85 Å2 / Biso mean: 19.9869 Å2 / Biso min: 5.83 Å2
Refinement stepCycle: final / Resolution: 1.45→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 16 97 1320
Biso mean--30.77 32.54 -
Num. residues----153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4498-1.50160.3186470.185681085727
1.5016-1.56170.2323820.16591233131541
1.5617-1.63280.21831060.16041781188760
1.6328-1.71890.20121540.14592724287891
1.7189-1.82660.21921700.13042987315799
1.8266-1.96760.17521870.12422990317799
1.9676-2.16560.1771400.115730173157100
2.1656-2.4790.15411660.129830073173100
2.479-3.12320.19451490.164230373186100
3.1232-44.93620.16561500.157630753225100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3817-0.11080.12670.26730.37360.38580.0332-0.1370.01330.3378-0.1092-0.20410.3235-0.1272-0.04720.1349-0.0124-0.04190.07190.00020.105723.299232.290922.0896
20.1243-0.14870.16160.0498-0.04270.15060.02110.16240.0328-0.06850.0082-0.074-0.06430.057900.0967-0.0054-0.00370.10480.00170.128220.731731.35426.8866
30.3078-0.0711-0.03320.2002-00.7865-0.03910.03570.00240.08340.0384-0.03040.05310.01350.00630.042-0.0123-0.00460.0701-0.00430.067817.789133.388914.2849
40.044-0.00920.02960.0394-0.03260.1390.27370.4258-0.0379-0.1917-0.2961-0.186-0.06060.199-0.01950.1370.0637-0.02360.2123-0.12030.179325.962916.98980.2571
50.0126-0.1580.01640.2406-0.30460.1910.0510.1049-0.0998-0.0247-0.07950.1916-0.0354-0.0310.07930.07250.0253-0.00240.0984-0.03830.092411.628832.05578.2416
60.19-0.09260.04720.2992-0.11590.399800.0171-0.1230.3198-0.12680.21010.4661-0.24730.00850.10720.01750.02650.158-0.07390.10298.191230.549911.7562
70.21750.0458-0.23760.1593-0.1890.2469-0.0915-0.0622-0.17090.1061-0.05930.07510.1727-0.1184-0.01480.1031-0.02120.03650.0886-0.00970.13811.3727.35616.3524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 43 )A25 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 86 )A44 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 94 )A87 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 122 )A95 - 122
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 141 )A123 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 165 )A142 - 165

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