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- PDB-4rha: Structure of the C-terminal domain of outer-membrane protein OmpA... -

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Basic information

Entry
Database: PDB / ID: 4rha
TitleStructure of the C-terminal domain of outer-membrane protein OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
ComponentsOuter membrane protein A
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ompA / putative peptidoglycan domain / outer membrane protein
Function / homology
Function and homology information


: / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / membrane => GO:0016020
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
ACETIC ACID / 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: 1.75 Å
AuthorsCuff, M.E. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references / Other ...Database references / Other / Source and taxonomy / Structure summary
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 4, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)32,10010
Polymers31,3452
Non-polymers7558
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Outer membrane protein A
hetero molecules

B: Outer membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,10010
Polymers31,3452
Non-polymers7558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z+1/31
Buried area3300 Å2
ΔGint-121 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.627, 58.627, 72.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Outer membrane protein A


Mass: 15672.464 Da / Num. of mol.: 2 / Fragment: OmpA_C domain (UNP residues 204-345)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Strain: 14028S / Gene: ompA / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: D0ZTJ5, UniProt: A0A0H2UKZ3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 2.5M Ammonium sulphate, 0.1M HEPES pH 7.5, 1.5% MPD, 20mM Magnesium acetate, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
ReflectionRedundancy: 6.2 % / Number: 176260 / Rmerge(I) obs: 0.066 / Χ2: 1.69 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 28244 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.755010.0645.1055.8
3.774.7510.0533.8136
3.293.7710.0644.136.1
2.993.2910.0673.466.2
2.782.9910.0672.6366.3
2.612.7810.0712.3126.4
2.482.6110.0721.8516.4
2.382.4810.0761.7096.4
2.282.3810.0781.4286.4
2.22.2810.0841.3226.4
2.142.210.0881.1526.4
2.072.1410.0960.9626.4
2.022.0710.1080.886.4
1.972.0210.120.756.4
1.931.9710.1370.636.4
1.891.9310.1730.5886.4
1.851.8910.1850.4676.4
1.811.8510.2180.4216.3
1.781.8110.2550.3685.9
1.751.7810.3030.3465.5
ReflectionResolution: 1.75→50 Å / Num. all: 28244 / Num. obs: 28244 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.689 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.785.50.3033.214360.346100
1.78-1.815.90.2554.214060.368100
1.81-1.856.30.2185.414270.421100
1.85-1.896.40.1856.914100.467100
1.89-1.936.40.17314030.588100
1.93-1.976.40.13714230.63100
1.97-2.026.40.1214200.75100
2.02-2.076.40.10814220.88100
2.07-2.146.40.09613970.962100
2.14-2.26.40.08813991.152100
2.2-2.286.40.08414421.322100
2.28-2.386.40.07814181.428100
2.38-2.486.40.07614151.709100
2.48-2.616.40.07214071.851100
2.61-2.786.40.07114192.312100
2.78-2.996.30.06714092.636100
2.99-3.296.20.06714343.4699.7
3.29-3.776.10.06414004.1399.7
3.77-4.7560.05314103.81399.2
4.75-505.80.06413475.10594.7

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0 / FOM acentric: 0.497 / FOM centric: 0 / Reflection: 0 / Reflection acentric: 18792 / Reflection centric: 0
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDR cullis acentricLoc acentricPower acentricReflection acentric
11.320.1018792
20.943.70.7518707
Phasing MAD set shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDResolution (Å)R cullis acentricLoc acentricPower acentricReflection acentric
112.5-501.110.2042
17.14-12.51.240.20298
15-7.141.280.20794
13.85-51.040.201441
13.13-3.851.030.102276
12.63-3.131.430.103361
12.27-2.631.70.104555
12-2.271.91006025
212.5-501.0519.30.4241
27.14-12.51.0110.40.84284
25-7.140.917.31.01779
23.85-50.946.80.831408
23.13-3.850.925.30.82260
22.63-3.130.913.50.833355
22.27-2.630.932.70.714555
22-2.270.982.30.526025
Phasing MAD set site

Atom type symbol: Se

IDB isoFract xFract yFract zOccupancyOccupancy iso
132.0739-0.004-0.044-0.1255.6380
235.9926-0.3950.278-0.2545.0850
337.6005-0.004-0.044-0.1264.241-0.148
437.8912-0.3950.278-0.2543.558-0.126
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-5000.21201484420
7.14-12.500.3702980
5-7.1400.624053491367940
3.85-500.52014410
3.13-3.8500.553022760
2.63-3.1300.587033610
2.27-2.6300.5330105385574445550
2-2.2700.38601098060250
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 28121
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.43-10053.80.832501
5.18-6.4341.30.93508
4.55-5.1846.10.943522
4.1-4.5546.40.947588
3.76-4.150.20.949630
3.5-3.7651.60.952692
3.28-3.545.60.948736
3.1-3.2849.30.941798
2.95-3.1450.943824
2.82-2.9545.70.942870
2.7-2.8245.10.938940
2.6-2.744.10.936915
2.5-2.646.50.9421015
2.42-2.5470.941018
2.35-2.4247.60.9371045
2.28-2.3550.40.9341085
2.21-2.28520.9331137
2.16-2.2151.50.9271148
2.1-2.1654.80.9241217
2.05-2.158.70.9251207
2.01-2.05600.9141238
1.96-2.0185.70.9191270
1.92-1.9688.70.911286
1.88-1.9290.90.8811302
1.85-1.88910.8721376
1.81-1.8588.60.8591389
1.78-1.8192.30.7811363
1.75-1.78900.6121501

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.31 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2094 / WRfactor Rwork: 0.1752 / FOM work R set: 0.9094 / SU B: 4.086 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1062 / SU Rfree: 0.1025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 1421 5.1 %RANDOM
Rwork0.1665 ---
obs0.1681 26698 99.65 %-
all-26698 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.26 Å2 / Biso mean: 37.487 Å2 / Biso min: 15.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 42 192 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192097
X-RAY DIFFRACTIONr_bond_other_d0.0010.021987
X-RAY DIFFRACTIONr_angle_refined_deg1.541.992854
X-RAY DIFFRACTIONr_angle_other_deg0.82134579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11625.48493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1951512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
X-RAY DIFFRACTIONr_mcbond_it1.92.4921075
X-RAY DIFFRACTIONr_mcbond_other1.8862.4871073
X-RAY DIFFRACTIONr_mcangle_it2.8063.7011353
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 105 -
Rwork0.215 1999 -
all-2104 -
obs--100 %
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)
12.66050.43980.70271.46270.22851.59010.1481-0.04530.05050.02390.0336-0.089-0.01850.1829-0.18170.0248-0.00360.02050.0511-0.02890.040838.37220.462822.5991
22.38140.0714-0.65221.55-0.3611.35390.0527-0.13870.1031-0.0601-0.03660.0473-0.07640.0189-0.0160.02140.0213-0.00360.0548-0.01090.006855.43138.934121.0383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A213 - 345
2X-RAY DIFFRACTION2B214 - 340

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