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- PDB-5kol: Crystal structure of the competence-damaged protein (CinA) superf... -

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Basic information

Entry
Database: PDB / ID: 5kol
TitleCrystal structure of the competence-damaged protein (CinA) superfamily protein ECK1530/EC0983 from Escherichia coli
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CinA / Competence-damaged protein / outer membrane biogenesis / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Disease
Function / homologyCinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta / ACETATE ION / Inactive PncC family protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsStogios, P.J. / Wawrak, Z. / Evdokimova, E. / Di Leo, R. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: To be published
Authors: Stogios, P.J.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,6778
Polymers73,4554
Non-polymers2224
Water12,160675
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8554
Polymers36,7282
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-22 kcal/mol
Surface area15600 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8224
Polymers36,7282
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-23 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.690, 89.150, 245.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-202-

ACT

21B-202-

ACT

31B-322-

HOH

41D-221-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 18363.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ydeJ, ECs2146, Z2161 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XB29
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5 M ammonium chloride, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.91→37.885 Å / Num. obs: 65002 / % possible obs: 99.2 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.1
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.838 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIXphasing
HKL-3000data scaling
Cootmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A9S

2a9s


Resolution: 1.91→37.885 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3302 5.1 %RANDOM
Rwork0.2065 ---
obs0.2088 64773 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→37.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 12 678 5830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075282
X-RAY DIFFRACTIONf_angle_d0.8377177
X-RAY DIFFRACTIONf_dihedral_angle_d19.6831888
X-RAY DIFFRACTIONf_chiral_restr0.054850
X-RAY DIFFRACTIONf_plane_restr0.004931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93730.61171260.55112351X-RAY DIFFRACTION92
1.9373-1.96620.39951340.40222423X-RAY DIFFRACTION94
1.9662-1.99690.35111170.31422521X-RAY DIFFRACTION100
1.9969-2.02970.31691200.28562638X-RAY DIFFRACTION100
2.0297-2.06470.31781400.28522516X-RAY DIFFRACTION100
2.0647-2.10220.3481520.27642570X-RAY DIFFRACTION100
2.1022-2.14270.30361350.26152555X-RAY DIFFRACTION100
2.1427-2.18640.28181360.2522597X-RAY DIFFRACTION100
2.1864-2.23390.31071330.27882500X-RAY DIFFRACTION98
2.2339-2.28590.41191400.35272361X-RAY DIFFRACTION92
2.2859-2.3430.28691480.24632570X-RAY DIFFRACTION100
2.343-2.40640.2841540.23182540X-RAY DIFFRACTION100
2.4064-2.47720.27781350.21582579X-RAY DIFFRACTION100
2.4772-2.55710.2581580.21662584X-RAY DIFFRACTION100
2.5571-2.64850.28521140.21352576X-RAY DIFFRACTION100
2.6485-2.75450.28661340.21472577X-RAY DIFFRACTION100
2.7545-2.87980.23911340.20992586X-RAY DIFFRACTION100
2.8798-3.03160.28911420.20782596X-RAY DIFFRACTION100
3.0316-3.22140.23221440.2042597X-RAY DIFFRACTION100
3.2214-3.470.26021350.18992622X-RAY DIFFRACTION100
3.47-3.81890.21841390.17372588X-RAY DIFFRACTION100
3.8189-4.37080.20191320.15082632X-RAY DIFFRACTION100
4.3708-5.50410.15771330.14982680X-RAY DIFFRACTION100
5.5041-37.89210.19661670.16762712X-RAY DIFFRACTION99

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