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- PDB-5ves: The 2.4A crystal structure of OmpA domain of OmpA from Salmonella... -

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Basic information

Entry
Database: PDB / ID: 5ves
TitleThe 2.4A crystal structure of OmpA domain of OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
ComponentsOuter membrane protein A
KeywordsMEMBRANE PROTEIN / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PROGRAM FOR THE CHARACTERIZATION OF SECRETED EFFECTOR PROTEINS / PCSEP
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein A
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTan, K. / Wu, R. / Jedrzejczak, R. / Adkins, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098248, GM109456 and GM094585 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi.
Authors: Tan, K. / Deatherage Kaiser, B.L. / Wu, R. / Cuff, M. / Fan, Y. / Bigelow, L. / Jedrzejczak, R.P. / Adkins, J.N. / Cort, J.R. / Babnigg, G. / Joachimiak, A.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein A
B: Outer membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5949
Polymers31,9212
Non-polymers6727
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-6 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.371, 109.371, 56.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Outer membrane protein A


Mass: 15960.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria)
Strain: 14028s / SGSC 2262 / Gene: ompA, STM14_1214 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: A0A0F6AZN3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M AMMONIUM SULFATE, 20% (W/V) PEG3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.4→48.5 Å / Num. obs: 15529 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.048 / Χ2: 1.359 / Net I/σ(I): 19.94
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 748 / CC1/2: 0.806 / Rpim(I) all: 0.322 / Χ2: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERH

4erh


Resolution: 2.4→48.454 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 836 5.4 %random
Rwork0.1862 ---
obs0.189 15473 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 35 49 2009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071992
X-RAY DIFFRACTIONf_angle_d1.1192697
X-RAY DIFFRACTIONf_dihedral_angle_d14.075737
X-RAY DIFFRACTIONf_chiral_restr0.067306
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55040.3331220.2532420X-RAY DIFFRACTION100
2.5504-2.74730.31211470.23322400X-RAY DIFFRACTION100
2.7473-3.02370.27141460.23142408X-RAY DIFFRACTION100
3.0237-3.46120.29791460.21012422X-RAY DIFFRACTION100
3.4612-4.36030.19571560.16562433X-RAY DIFFRACTION100
4.3603-48.46370.19661190.15042554X-RAY DIFFRACTION100
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)
15.09312.9114-0.91373.5505-3.84495.9381-0.0288-0.27030.01390.19080.0440.0451-0.3767-0.5017-0.05820.46280.17040.04140.3961-0.04770.316315.150252.146710.6766
25.471-3.67413.0016.853-4.09932.6285-0.748-1.9088-1.04611.09531.26470.65640.1366-0.1-0.53870.63480.15530.18731.06520.14410.686716.584236.570420.9928
33.07180.05291.13293.6643-1.75278.3153-0.1566-0.1438-0.07380.0686-0.1117-0.3545-0.01340.27570.29440.27740.09010.01650.39060.00080.36822.087347.06286.135
42.58332.9514-1.81885.2295-4.20648.526-0.09690.3980.1863-0.52670.33830.09770.3255-0.7679-0.22490.30910.0905-0.01180.4464-0.01130.37488.900950.7916-8.7993
57.1271-1.92493.66574.7923-4.94495.5132-0.0588-0.3768-0.9564-0.00690.3002-0.20190.482-0.5255-0.26240.40260.11850.04850.45370.07210.398614.255841.64618.3309
65.98110.3083-1.38332.3277-2.11292.2374-0.10230.50820.58350.08260.3376-0.1128-0.5833-0.4616-0.21250.49380.03410.0190.41220.00350.320516.647871.2612-26.6412
75.16630.42480.79786.0591-5.64867.80510.2705-0.22840.0106-0.5644-0.1278-0.42051.21350.3548-0.20110.54450.00690.06520.4481-0.08420.466719.920257.1989-18.2701
86.51240.7687-0.81844.4497-6.21639.032-0.34090.7802-0.4322-0.7705-0.1936-0.330.156-1.01610.45090.60270.01080.00280.5217-0.12550.383115.290363.6579-32.9075
94.60991.1145-1.09393.7125-1.12892.01920.07680.6360.2773-0.1210.2521-0.1117-0.69590.4039-0.40680.412-0.06630.00150.40740.00030.528724.638271.7257-25.3225
104.95790.80323.49392.9578-0.08692.71880.06460.20290.1849-0.008-0.1922-0.33920.49040.41540.16070.31280.01270.07040.3712-0.03350.412526.564163.0077-22.6081
117.51770.0375-3.514.36891.57182.4428-0.16630.2941-0.146-0.48650.0005-0.8051-0.72241.5530.10660.4466-0.11050.04660.4670.02310.51928.813169.5431-27.3603
126.40693.2835-0.18673.35642.31723.2183-0.5175-0.63760.44360.66710.3195-0.05020.0817-0.40880.07730.62410.1588-0.10150.39710.04160.408914.90674.8481-5.6692
131.15553.0035-2.71798.5712-8.1428.0417-0.20230.0707-0.19170.15770.1088-0.5539-0.1143-0.15360.09780.40810.13030.01960.3729-0.00280.329112.662367.9812-8.4578
145.88461.1345-0.93277.5177-3.91242.0890.01220.85760.6157-0.19140.2031-0.0293-0.90350.2728-0.30580.5148-0.02840.05850.51460.13010.447320.798873.4767-27.5544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 194 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 320 )
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 205 )
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 215 through 229 )
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 271 )
11X-RAY DIFFRACTION11chain 'B' and (resid 272 through 286 )
12X-RAY DIFFRACTION12chain 'B' and (resid 287 through 299 )
13X-RAY DIFFRACTION13chain 'B' and (resid 300 through 310 )
14X-RAY DIFFRACTION14chain 'B' and (resid 311 through 321 )

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