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- PDB-5cbo: Fusion protein of mbp3-16 and B4 domain of protein A from staphyl... -

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Basic information

Entry
Database: PDB / ID: 5cbo
TitleFusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus
Componentsmbp3-16,Immunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / Fusion / alpha helix / cross-linker
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Ankyrin repeat-containing domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciessynthetic construct (others)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.802 Å
AuthorsJeong, W.H. / Lee, H. / Song, D.H. / Lee, J.O.
CitationJournal: Nat Commun / Year: 2016
Title: Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.
Authors: Jeong, W.H. / Lee, H. / Song, D.H. / Eom, J.H. / Kim, S.C. / Lee, H.S. / Lee, H. / Lee, J.O.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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_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

Downloads & links

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Assembly

Deposited unit
A: mbp3-16,Immunoglobulin G-binding protein A
B: mbp3-16,Immunoglobulin G-binding protein A
C: mbp3-16,Immunoglobulin G-binding protein A
D: mbp3-16,Immunoglobulin G-binding protein A
E: mbp3-16,Immunoglobulin G-binding protein A
F: mbp3-16,Immunoglobulin G-binding protein A
G: mbp3-16,Immunoglobulin G-binding protein A
H: mbp3-16,Immunoglobulin G-binding protein A
I: mbp3-16,Immunoglobulin G-binding protein A
J: mbp3-16,Immunoglobulin G-binding protein A
K: mbp3-16,Immunoglobulin G-binding protein A
L: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)229,12112
Polymers229,12112
Non-polymers00
Water61334
1
A: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: mbp3-16,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.497, 220.393, 85.524
Angle α, β, γ (deg.)90.00, 59.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
12
22
32
42
52
62
72
82
92
102
112
122

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 12:135
211chain B and resid 12:135
311chain C and resid 12:135
411chain D and resid 12:135
511chain E and resid 12:135
611chain F and resid 12:135
711chain G and resid 12:135
811chain H and resid 12:135
911chain I and resid 12:135
1011chain J and resid 12:135
1111chain K and resid 12:135
1211chain L and resid 12:135
112chain A and resid 1218:1269
212chain B and resid 1218:1269
312chain C and resid 1218:1269
412chain D and resid 1218:1269
512chain E and resid 1218:1269
612chain F and resid 1218:1269
712chain G and resid 1218:1269
812chain H and resid 1218:1269
912chain I and resid 1218:1269
1012chain J and resid 1218:1269
1112chain K and resid 1218:1269
1212chain L and resid 1218:1269

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.505114, 0.006222, 0.86303), (-0.001761, -0.999965, 0.00824), (0.863051, -0.005682, -0.505085)-0.072455, -55.309101, -0.085753
2given(0.11132, 0.041015, 0.992938), (0.017429, -0.999075, 0.039315), (0.993632, 0.012929, -0.111932)1.93747, -111.610001, 1.06379
3given(0.917271, -0.036578, -0.39658), (0.038052, 0.999267, -0.004154), (0.396442, -0.01128, 0.917991)-0.521446, -56.308399, 0.470351
4given(-0.508995, 0.048558, 0.859399), (-0.00522, 0.998215, -0.059493), (-0.860754, -0.034767, -0.507833)5.25253, 0.079805, 7.50526
5given(-0.999926, 0.010163, 0.006736), (-0.009587, -0.996699, 0.080613), (0.007533, 0.080542, 0.996723)9.28422, -55.730301, 2.42939
6given(-0.912306, -0.002153, -0.409503), (-0.028157, -0.99729, 0.067973), (-0.408539, 0.073542, 0.909773)9.293, -111.439003, 6.11381
7given(-0.107054, 0.04159, 0.993383), (-0.01333, 0.998975, -0.043261), (-0.994164, -0.017873, -0.10639)2.96885, -55.9482, 9.41229
8given(-0.498953, -0.020214, -0.866393), (0.046594, 0.997656, -0.05011), (0.865376, -0.065371, -0.496842)8.30703, -0.257576, -1.40197
9given(0.487747, -0.051733, -0.871451), (-0.054071, -0.998116, 0.028989), (-0.871309, 0.032981, -0.489626)2.57924, -55.136002, 9.38542
10given(0.80713, -0.030595, -0.58958), (-0.03675, -0.999323, 0.001548), (-0.589228, 0.020418, -0.807708)1.39696, -111.403, 10.6585
11given(-0.807945, -0.000579, -0.589257), (0.04802, 0.996609, -0.06682), (0.587297, -0.082283, -0.805178)9.21073, -56.348701, 2.0878
12given(0.499843, 0.013814, 0.866006), (0.018531, -0.999814, 0.005252), (0.865918, 0.013423, -0.500006)0.188621, -55.675999, 0.226138
13given(0.065514, 0.02627, 0.997506), (0.046138, -0.998664, 0.02327), (0.996784, 0.044498, -0.066639)1.30729, -111.630997, 2.41849
14given(0.895732, 0.003419, -0.444582), (0.00495, 0.999832, 0.017663), (0.444568, -0.018022, 0.895564)-0.583545, -55.523998, -0.442244
15given(-0.483367, 0.064141, 0.873065), (-0.011781, 0.996745, -0.07975), (-0.875338, -0.048834, -0.481038)5.96877, 0.407219, 6.42769
16given(-0.999997, 0.000545, -0.002266), (-0.00077, -0.994942, 0.100445), (-0.0022, 0.100446, 0.99494)9.40711, -55.476002, 2.71525
17given(-0.909773, -0.01484, -0.41484), (-0.044372, -0.990158, 0.132732), (-0.412727, 0.139163, 0.900161)8.37193, -110.875, 10.6314
18given(-0.061326, 0.101372, 0.992957), (-0.073022, 0.991707, -0.105755), (-0.995443, -0.078993, -0.053415)2.32684, -54.5326, 9.68488
19given(-0.503376, 0.002326, -0.864064), (0.066842, 0.997105, -0.036256), (0.861478, -0.076006, -0.502074)9.45459, -0.116938, -2.00944
20given(0.51681, -0.05102, -0.854579), (-0.072485, -0.997246, 0.015703), (-0.853026, 0.053829, -0.519085)2.62745, -55.197102, 9.16536
21given(0.832464, -0.13544, -0.53727), (-0.146064, -0.989008, 0.023003), (-0.53448, 0.059327, -0.843096)-5.80187, -108.690002, 12.3763
22given(-0.819072, 0.021418, -0.57329), (0.098264, 0.989773, -0.103414), (0.565212, -0.141038, -0.8128)9.24934, -55.976601, 2.83196

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Components

#1: Antibody
mbp3-16,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 19093.391 Da / Num. of mol.: 12 / Fragment: B4 domain (UNP RESIDUES 102-153) / Mutation: D1219A, S1222A, E1226C, N1229H, E1236A
Source method: isolated from a genetically manipulated source
Details: Fusion protein of mbp3-16 and B4 domain (residues 102-153) of protein A
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: hexagonal plate
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5
Details: 34% w/v PPG P-400 10mM Hexaamine cobalt(III) chloride
Temp details: store at 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,h-l / Fraction: 0.46
ReflectionResolution: 2.8→50 Å / Num. obs: 62318 / % possible obs: 93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 / Χ2: 1.342 / Net I/av σ(I): 25.305 / Net I/σ(I): 16.1 / Num. measured all: 199816
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.93.10.15255161.27482.2
2.9-3.023.10.12857131.24385.1
3.02-3.153.10.10159321.28288.3
3.15-3.3230.08260951.22291.6
3.32-3.533.10.06362131.22693.2
3.53-3.83.10.04864201.24996.3
3.8-4.183.20.04264891.28997.6
4.18-4.793.30.03866601.2998.5
4.79-6.033.50.04366721.42399.7
6.03-503.50.04166081.76197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CBN

5cbn


Resolution: 2.802→33.06 Å / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 26.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2535 2068 3.32 %
Rwork0.2035 --
obs0.2075 62287 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16116 0 0 34 16150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916404
X-RAY DIFFRACTIONf_angle_d1.02422224
X-RAY DIFFRACTIONf_dihedral_angle_d17.2875916
X-RAY DIFFRACTIONf_chiral_restr0.0422460
X-RAY DIFFRACTIONf_plane_restr0.0052964
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A938X-RAY DIFFRACTIONPOSITIONAL
12B938X-RAY DIFFRACTIONPOSITIONAL0.044
13C938X-RAY DIFFRACTIONPOSITIONAL0.093
14D938X-RAY DIFFRACTIONPOSITIONAL0.05
15E938X-RAY DIFFRACTIONPOSITIONAL0.052
16F938X-RAY DIFFRACTIONPOSITIONAL0.051
17G938X-RAY DIFFRACTIONPOSITIONAL0.051
18H938X-RAY DIFFRACTIONPOSITIONAL0.048
19I938X-RAY DIFFRACTIONPOSITIONAL0.051
110J938X-RAY DIFFRACTIONPOSITIONAL0.053
111K938X-RAY DIFFRACTIONPOSITIONAL0.051
112L938X-RAY DIFFRACTIONPOSITIONAL0.052
21A405X-RAY DIFFRACTIONPOSITIONAL
22B405X-RAY DIFFRACTIONPOSITIONAL0.04
23C405X-RAY DIFFRACTIONPOSITIONAL0.049
24D405X-RAY DIFFRACTIONPOSITIONAL0.05
25E405X-RAY DIFFRACTIONPOSITIONAL0.051
26F405X-RAY DIFFRACTIONPOSITIONAL0.053
27G405X-RAY DIFFRACTIONPOSITIONAL0.05
28H405X-RAY DIFFRACTIONPOSITIONAL0.051
29I405X-RAY DIFFRACTIONPOSITIONAL0.052
210J405X-RAY DIFFRACTIONPOSITIONAL0.049
211K405X-RAY DIFFRACTIONPOSITIONAL0.05
212L405X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8058-2.87590.35851170.23923760X-RAY DIFFRACTION79
2.8759-2.95360.28281270.24013941X-RAY DIFFRACTION81
2.9536-3.04040.36911190.23153929X-RAY DIFFRACTION84
3.0404-3.13840.24991370.22654063X-RAY DIFFRACTION85
3.1384-3.25040.26631390.21764128X-RAY DIFFRACTION88
3.2504-3.38030.29991500.21264285X-RAY DIFFRACTION89
3.3803-3.53390.24821480.20364337X-RAY DIFFRACTION91
3.5339-3.71980.22011490.20164432X-RAY DIFFRACTION93
3.7198-3.95230.26031420.20054406X-RAY DIFFRACTION94
3.9523-4.25640.26331400.19534554X-RAY DIFFRACTION95
4.2564-4.6830.22991490.18294551X-RAY DIFFRACTION95
4.683-5.35650.21821590.19734638X-RAY DIFFRACTION96
5.3565-6.73310.30681340.22814607X-RAY DIFFRACTION97
6.7331-27.99710.21141540.19164565X-RAY DIFFRACTION95
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)
10.1151-0.01820.07430.1182-0.05280.31560.00910.05530.0155-0.0386-0.0503-0.047-0.03430.0579-0.00780.05980.0537-0.02650.32470.0211-0.018618.3747-43.320118.1349
20.1734-0.0674-0.12190.29490.02160.25720.0154-0.03760.03290.0376-0.0186-0.0280.0172-0.0054-0.02970.0808-0.01730.07930.3634-0.03510.043724.9449-12.01896.8254
30.52840.0915-0.17350.45470.05740.43390.0204-0.2426-0.04710.11390.0089-0.01120.10150.09550.02430.14370.08840.00350.4666-0.07160.106219.825-67.482817.013
40.1922-0.25060.07680.9273-0.30631.0045-0.12830.03830.14090.0268-0.0798-0.2059-0.19270.42510.0920.1696-0.0448-0.0030.4778-0.03940.137924.586212.24398.5386
50.06770.0482-0.01320.19680.04420.0808-0.0306-0.12820.01790.09690.02-0.01130.0002-0.0604-0.00020.04260.0255-0.1150.37120.07930.0866-15.4651-43.02268.428
60.1672-0.0057-0.00140.1505-0.070.03470.01-0.2510.08460.13520.0582-0.001-0.0675-0.03390.04310.1666-0.01960.02210.5003-0.04630.0448-9.0216-10.97916.6542
70.065-0.0117-0.11280.5758-0.00681.30070.0382-0.0021-0.00150.0371-0.02720.13440.1508-0.3904-0.10960.2837-0.0690.00380.44580.12530.1119-15.1277-67.122111.9001
81.0697-0.14160.08180.6342-0.35170.1973-0.1708-0.44640.23640.23720.03260.1231-0.1531-0.16560.10020.18970.1089-0.05050.4009-0.14470.3431-10.317413.33513.6069
90.06250.06980.03110.1192-0.05220.2115-0.02530.1088-0.0459-0.04960.0346-0.07210.09830.20030.05290.0990.06180.05180.5089-0.05490.06589.9385-44.3649-16.213
100.2533-0.03460.0710.231-0.00640.2199-0.00020.1543-0.0123-0.064-0.0255-0.05570.01940.1122-0.06840.00540.018-0.0240.35830.00610.0221-0.4784-12.3608-17.5786
110.24730.2380.34160.4760.19820.55680.05640.2443-0.1905-0.00080.0942-0.21050.22920.3165-0.28330.31540.1262-0.1520.431-0.19290.2386.6575-68.7442-15.6298
120.35530.1914-0.42960.91820.02450.60890.13530.31240.1685-0.2201-0.06940.1009-0.0048-0.1647-0.11420.1854-0.040.01580.41050.09930.11432.721811.7144-19.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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