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- PDB-4erh: The crystal structure of OmpA domain of OmpA from Salmonella ente... -

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Basic information

Entry
Database: PDB / ID: 4erh
TitleThe 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 / Outer membrane protein A
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 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)
CitationJournal: To be Published
Title: The crystal structure of OmpA domain of OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Authors: Tan, K. / Wu, R. / Jedrzejczak, R. / Adkins, J. / Joachimiak, A.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Structure summary

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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)32,4868
Polymers31,9212
Non-polymers5646
Water95553
1
A: Outer membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2454
Polymers15,9611
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2414
Polymers15,9611
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Outer membrane protein A
hetero molecules

B: Outer membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4868
Polymers31,9212
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
Buried area2430 Å2
ΔGint-50 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.435, 109.435, 56.392
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsExperimentally unknown. The domain is predicted to be monomeric.

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Components

#1: Protein Outer membrane protein A


Mass: 15960.742 Da / Num. of mol.: 2 / Fragment: UNP residues 205-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: ompA, STM14_1214 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D0ZTJ5, UniProt: A0A0F6AZN3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium sulfate, 20% (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97917, 0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979291
ReflectionResolution: 2.52→49 Å / Num. all: 13436 / Num. obs: 13436 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 44.69 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.9
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.67 / Num. unique all: 687 / Rsym value: 0.023 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.52→48.462 Å / SU ML: 0.84 / σ(F): 1.34 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 661 4.93 %Random
Rwork0.2004 ---
obs0.2037 13403 99.81 %-
all-13403 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.764 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0396 Å2-0 Å2-0 Å2
2--6.0396 Å20 Å2
3----12.0792 Å2
Refinement stepCycle: LAST / Resolution: 2.52→48.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 33 53 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082020
X-RAY DIFFRACTIONf_angle_d1.0642720
X-RAY DIFFRACTIONf_dihedral_angle_d17.273767
X-RAY DIFFRACTIONf_chiral_restr0.062308
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5198-2.71440.4361350.31122495X-RAY DIFFRACTION99
2.7144-2.98750.32021280.25692525X-RAY DIFFRACTION100
2.9875-3.41970.31271260.21692548X-RAY DIFFRACTION100
3.4197-4.3080.23271410.18422527X-RAY DIFFRACTION100
4.308-48.47090.22151310.16652647X-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)
15.8123-2.35941.11343.33360.77522.93050.3658-0.84130.84980.3935-0.1427-0.8469-0.55270.2568-0.67390.41770.02240.00660.4605-0.11060.435823.180763.191617.5608
22.1065-1.227-0.12863.2969-2.77856.6363-0.13940.7646-0.2975-0.06320.31510.4275-0.6573-1.6583-0.09920.33720.1068-0.08190.65190.02190.257416.487153.565615.415
36.40.5771-2.26654.0425-0.54144.46470.1454-0.1616-0.0623-0.0457-0.3685-0.1946-0.10950.1710.00460.22130.0219-0.07990.2615-0.0190.177725.557255.477923.287
45.08151.4822-0.62255.7701-0.12077.6967-0.19770.5999-0.0816-0.35790.0663-0.44320.27540.35590.32130.30320.12990.04260.3009-0.00160.219627.080751.453417.2594
58.95422.2407-0.63565.4777-1.05486.83750.5297-0.61050.31130.5333-0.33230.3193-1.3676-0.2404-0.2270.55210.0713-0.04040.3321-0.02110.227117.339663.351738.6089
65.3793-0.1434-2.6232.45-0.73694.40730.2267-0.15920.39150.0083-0.05660.1298-0.98530.1909-0.04950.30160.1703-0.0310.39920.03880.285518.603160.550127.4308
74.1163-2.16470.22057.0528-1.22052.1315-0.3827-0.22780.1667-0.03010.3571-0.16890.0346-0.31120.08160.3669-0.02190.05370.4696-0.09710.249210.774377.80432.3478
89.4058-2.34095.98767.3415-2.9859.2690.1068-1.51190.00860.3716-0.740.25020.8176-0.9460.59480.54450.05950.11780.7323-0.06650.22778.066276.157242.3572
98.3022-4.4851.88435.34361.85413.24941.3757-3.1559-1.49261.8367-0.2025-0.867-0.96632.0063-1.68310.9904-0.3028-0.12591.26420.0870.721124.688380.967751.4844
103.73121.41020.18262.83851.04613.63670.07650.40350.302-0.15490.0751-0.25450.47350.5841-0.13890.2933-0.025-0.00140.3571-0.08780.280217.900280.31526.6362
116.40851.4477-0.94993.8341-1.48932.7598-0.29940.28260.54920.9831-0.0343-0.2529-0.3434-0.57550.1880.5036-0.0281-0.00680.1572-0.09290.326113.206186.24132.0299
125.85690.30790.10865.06041.31182.5751-0.2389-0.63260.31930.8222-0.123-0.6002-0.21461.6720.11680.51020.0308-0.10770.5982-0.03090.462620.491684.367735.8256
139.45950.6525-3.02814.80930.19411.0019-0.2720.4038-0.4001-1.0311-0.2045-0.10110.09660.08820.2860.58110.11430.04830.50750.140.309316.96569.675814.1996
143.01151.33512.40953.375-0.66236.0683-0.28050.1351-0.2995-0.56480.06680.3371.41020.24770.09870.57350.09090.04780.2201-0.02620.286910.494671.671217.8687
150.68930.15910.44570.3571-0.66432.96450.8305-0.66750.28790.5357-0.4738-0.34051.44560.96440.08250.57140.0483-0.10350.6427-0.04730.455819.81175.957337.9844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 213:226)
2X-RAY DIFFRACTION2chain 'A' and (resseq 227:250)
3X-RAY DIFFRACTION3chain 'A' and (resseq 251:276)
4X-RAY DIFFRACTION4chain 'A' and (resseq 277:305)
5X-RAY DIFFRACTION5chain 'A' and (resseq 306:320)
6X-RAY DIFFRACTION6chain 'A' and (resseq 321:341)
7X-RAY DIFFRACTION7chain 'B' and (resseq 215:235)
8X-RAY DIFFRACTION8chain 'B' and (resseq 236:250)
9X-RAY DIFFRACTION9chain 'B' and (resseq 251:257)
10X-RAY DIFFRACTION10chain 'B' and (resseq 258:270)
11X-RAY DIFFRACTION11chain 'B' and (resseq 271:292)
12X-RAY DIFFRACTION12chain 'B' and (resseq 293:308)
13X-RAY DIFFRACTION13chain 'B' and (resseq 309:320)
14X-RAY DIFFRACTION14chain 'B' and (resseq 321:331)
15X-RAY DIFFRACTION15chain 'B' and (resseq 332:342)

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