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- PDB-5wtl: Crystal structure of the periplasmic portion of outer membrane pr... -

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Basic information

Entry
Database: PDB / ID: 5wtl
TitleCrystal structure of the periplasmic portion of outer membrane protein A (OmpA) from Capnocytophaga gingivalis
ComponentsOmpA family protein
KeywordsMEMBRANE PROTEIN / prokaryote / TT3R / TSP3 / Calcium-binding motif
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / cell adhesion / calcium ion binding
Similarity search - Function
Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / Outer membrane protein, bacterial / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / Outer membrane protein, bacterial / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
Biological speciesCapnocytophaga gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsDai, S. / Tan, K. / Ye, S. / Zhang, R.
CitationJournal: Cell Calcium / Year: 2017
Title: Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability.
Authors: Dai, S. / Sun, C. / Tan, K. / Ye, S. / Zhang, R.
History
DepositionDec 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2Nov 8, 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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpA family protein
B: OmpA family protein
C: OmpA family protein
D: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,93848
Polymers111,9084
Non-polymers2,03144
Water8,017445
1
A: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,41812
Polymers27,9771
Non-polymers44111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,47412
Polymers27,9771
Non-polymers49711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,70914
Polymers27,9771
Non-polymers73213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,33810
Polymers27,9771
Non-polymers3619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.205, 87.343, 185.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
OmpA family protein


Mass: 27976.947 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 195-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Gene: CAPGI0001_0903 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M2E7
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.0, 200 mM Ca(Ac)2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.298→42.509 Å / Num. obs: 53087 / % possible obs: 98.6 % / Redundancy: 3.4 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.34 Å

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Processing

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

4erh


Resolution: 2.298→42.509 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2551 2700 5.09 %
Rwork0.203 --
obs0.2057 53041 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.298→42.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7675 0 63 445 8183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168109
X-RAY DIFFRACTIONf_angle_d2.07211069
X-RAY DIFFRACTIONf_dihedral_angle_d11.1373081
X-RAY DIFFRACTIONf_chiral_restr0.0531100
X-RAY DIFFRACTIONf_plane_restr0.0031489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2978-2.33960.32741350.25932575X-RAY DIFFRACTION98
2.3396-2.38460.31141450.24712611X-RAY DIFFRACTION99
2.3846-2.43330.31421480.24962653X-RAY DIFFRACTION99
2.4333-2.48620.27551460.24552614X-RAY DIFFRACTION100
2.4862-2.5440.3531310.2442647X-RAY DIFFRACTION99
2.544-2.60760.32061370.24352642X-RAY DIFFRACTION99
2.6076-2.67810.28741270.23162648X-RAY DIFFRACTION100
2.6781-2.75690.29081230.23082677X-RAY DIFFRACTION100
2.7569-2.84590.29821290.22792680X-RAY DIFFRACTION100
2.8459-2.94760.31991490.22282637X-RAY DIFFRACTION99
2.9476-3.06560.31051420.22452675X-RAY DIFFRACTION99
3.0656-3.2050.29051520.21522637X-RAY DIFFRACTION99
3.205-3.37390.23521450.20922668X-RAY DIFFRACTION99
3.3739-3.58520.24141750.19572621X-RAY DIFFRACTION99
3.5852-3.86190.22441400.17862679X-RAY DIFFRACTION99
3.8619-4.25020.23041650.17482653X-RAY DIFFRACTION99
4.2502-4.86440.20061260.16612697X-RAY DIFFRACTION98
4.8644-6.12580.24411470.18792638X-RAY DIFFRACTION96
6.1258-42.51610.21431380.19112689X-RAY DIFFRACTION93
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)
11.4024-1.1229-0.95080.89690.81722.8303-0.3160.6689-0.8481-1.65330.0823-0.76270.95870.61110.11471.54140.30020.31581.2306-0.01110.810427.276723.7059-42.1242
21.9228-0.23120.26241.51880.40491.56410.07140.4018-0.1561-0.7361-0.0714-0.4477-0.00070.04430.02550.5660.09750.08570.3066-0.04780.419519.938831.1025-24.1152
3-0.35990.39690.4595-0.62170.44133.6364-0.0153-0.2196-0.13570.14390.0209-0.20831.04130.0117-0.09190.71930.1183-0.04620.6152-0.00470.392916.050635.716117.2301
42.7222-0.82750.28132.80550.63152.4141-0.13950.1044-0.15590.08870.21650.45030.157-0.4324-0.09690.2392-0.0676-0.04980.28040.07630.406410.609632.832763.8631
52.6977-1.1611-1.25982.02391.72832.7968-0.1408-0.0435-0.2531-0.02760.12390.5017-0.1457-0.3477-0.1880.2109-0.05390.00310.3820.12460.45727.683740.316466.947
60.3471-0.64090.40854.49161.20851.7398-0.5994-0.474-0.42030.2923-0.4490.23920.0390.18060.63160.70090.16820.371.2390.52521.7705-11.801324.74155.9872
71.89021.3735-0.93521.0697-0.76270.5162-0.1791-0.3863-0.06090.49030.61781.08340.3774-1.2145-0.57380.8796-0.16690.08620.73410.21220.8218-1.786730.0738150.2866
80.30840.6737-1.2847-0.1357-0.58722.18350.05610.2339-0.0648-0.0812-0.05660.14690.3177-0.2322-0.06390.51490.0879-0.00270.48330.03530.404415.387738.1857120.8064
92.5422-0.5101-1.42890.4330.0712.3416-0.18220.2798-0.4145-0.91940.37220.38710.1213-0.7081-0.18490.8465-0.0992-0.1890.53220.00580.395930.433738.586485.7205
102.9486-0.0248-0.04432.6057-0.99272.7052-0.00040.12730.0288-0.26790.01-0.2971-0.0160.4589-0.02810.2883-0.04220.00870.2575-0.03710.289434.605331.475361.1132
111.8776-0.4511-0.67811.74980.460.3283-0.6154-0.25260.43140.80940.4049-0.0178-0.15410.18150.15510.68270.1693-0.04410.36830.00310.48689.67479.429893.7403
123.841-0.9630.27382.0897-0.67152.36550.13620.16610.1441-0.0605-0.1728-0.1772-0.07580.3127-0.00950.20290.01-0.03480.2325-0.02640.208530.73229.9525164.0668
131.6818-1.03551.22221.71420.36082.8157-0.0889-0.10960.02570.7836-0.1942-0.9612-0.64590.3550.08191.316-0.7814-0.86251.50760.29050.603829.611718.4548268.2277
143.34531.66660.22252.6130.75692.5992-0.22970.3762-0.0448-0.4318-0.1129-0.11390.4262-0.23070.25040.6458-0.0846-0.02530.3417-0.02130.399119.40910.9671243.8753
150.2992-0.18-0.6340.2028-0.01973.47050.5516-0.55280.01690.9062-0.2185-0.473-1.4391-0.0842-0.14391.5758-0.4424-0.06881.07040.01120.596910.2118.5886206.8387
161.66990.0233-0.54462.10010.73182.6811-0.0015-0.05880.08-0.03970.01950.2874-0.084-0.6225-0.05680.2540.0642-0.04330.40010.04390.40397.17749.2505167.3037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 198 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 337 )
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 439 )
5X-RAY DIFFRACTION5chain 'A' and (resid 440 through 455 )
6X-RAY DIFFRACTION6chain 'B' and (resid 198 through 213 )
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 235 )
8X-RAY DIFFRACTION8chain 'B' and (resid 236 through 316 )
9X-RAY DIFFRACTION9chain 'B' and (resid 317 through 337 )
10X-RAY DIFFRACTION10chain 'B' and (resid 338 through 455 )
11X-RAY DIFFRACTION11chain 'C' and (resid 196 through 304 )
12X-RAY DIFFRACTION12chain 'C' and (resid 305 through 455 )
13X-RAY DIFFRACTION13chain 'D' and (resid 209 through 217 )
14X-RAY DIFFRACTION14chain 'D' and (resid 218 through 289 )
15X-RAY DIFFRACTION15chain 'D' and (resid 290 through 321 )
16X-RAY DIFFRACTION16chain 'D' and (resid 322 through 455 )

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