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Basic information

Entry
Database: PDB / ID: 4jdz
TitleStructures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
Components(Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD) x 2
KeywordsCELL ADHESION / receptor / surface / MSCRAMM / Staphylococcus aureus
Function / homologyImmunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Ge, J. / Yang, M.
CitationJournal: Protein Cell / Year: 2013
Title: Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
Authors: Wang, X. / Ge, J. / Liu, B. / Hu, Y. / Yang, M.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Refinement description
Category: refine / reflns_shell / struct_ref_seq_dif
Item: _refine.pdbx_starting_model / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD
A: Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,91210
Polymers96,5912
Non-polymers3218
Water8,935496
1
B: Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9115
Polymers48,7501
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0025
Polymers47,8411
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.41, 73.88, 90.03
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD


Mass: 48750.188 Da / Num. of mol.: 1 / Fragment: UNP residues 235-678 / Mutation: D20I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: TCH60 / Gene: sdrD, HMPREF0772_12627 / Production host: Escherichia coli (E. coli) / References: UniProt: E5QTK7
#2: Protein Ser-Asp rich fibrinogen/bone sialoprotein-binding protein SdrD


Mass: 47841.309 Da / Num. of mol.: 1 / Fragment: UNP residues 235-673 / Mutation: D19I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: TCH60 / Gene: sdrD, HMPREF0772_12627 / Production host: Escherichia coli (E. coli) / References: UniProt: E5QTK7
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQRES CONFLICTS HAVE CAUSED BY REFINEMENT ARTIFACTS.

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Calcium chloride dihydrate, 0.1M HEPES sodium(7.5), 20%(v/v) 2-Propanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MAR225 / Detector: CCD / Date: Jun 13, 2009
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 55836 / Rmerge(I) obs: 0.062 / Net I/σ(I): 33
Reflection shell
Resolution (Å)Diffraction-ID
2.1-2.141
2.14-2.181
2.18-2.221
2.22-2.261
2.26-2.311
2.31-2.371
2.37-2.421
2.42-2.491
2.49-2.561
2.56-2.651
2.65-2.741
2.74-2.851
2.85-2.981
2.98-3.141
3.14-3.591
3.59-3.951
3.95-4.521
4.52-5.71

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Processing

Software
NameClassification
HKL-2000data collection
DMmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2315 2753 5.08 %
Rwork0.1847 --
all0.187 --
obs0.187 55836 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 8 496 7258
LS refinement shell
Resolution (Å)Refine-IDTotal num. of bins used
2.1-2.132X-RAY DIFFRACTION20
2.132-2.1707X-RAY DIFFRACTION20
2.1707-2.2124X-RAY DIFFRACTION20
2.2124-2.2576X-RAY DIFFRACTION20
2.2576-2.3067X-RAY DIFFRACTION20
2.3067-2.3603X-RAY DIFFRACTION20
2.3603-2.4193X-RAY DIFFRACTION20
2.4193-2.4847X-RAY DIFFRACTION20
2.4847-2.5577X-RAY DIFFRACTION20
2.5577-2.6403X-RAY DIFFRACTION20
2.6403-2.7346X-RAY DIFFRACTION20
2.7346-2.844X-RAY DIFFRACTION20
2.844-2.9733X-RAY DIFFRACTION20
2.9733-3.1299X-RAY DIFFRACTION20
3.1299-3.3257X-RAY DIFFRACTION20
3.3257-3.5821X-RAY DIFFRACTION20
3.5821-3.9418X-RAY DIFFRACTION20
3.9418-4.5105X-RAY DIFFRACTION20
4.5105-5.676X-RAY DIFFRACTION20
5.676-29.4706X-RAY DIFFRACTION20
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)
11.2509-0.5254-0.30140.44770.90271.64330.5140.46220.1545-0.5931-0.61890.2217-0.8938-0.11480.13380.68580.24-0.03770.56720.10080.302723.64870.638516.9717
20.90420.0581-0.59641.2903-0.24020.42910.10220.02210.3443-0.7585-0.3391-0.5051-1.00870.69370.06851.0414-0.14010.03960.39340.18110.400835.02756.31117.1894
30.69120.1627-0.97980.81960.1631.04340.44480.17840.0960.1178-0.6827-0.9141-1.63521.202-0.07841.1255-0.25730.15150.80180.3030.553740.59045.556910.1787
41.1569-0.2144-0.12971.30591.27791.89260.15630.5590.0137-0.3553-0.32610.2005-0.8085-0.41870.14940.40760.2103-0.04250.39750.03380.212321.4019-2.121828.4149
50.4544-0.019-0.02382.47920.15580.3891-0.00230.00710.009-0.0462-0.0636-0.16020.03080.10180.08710.16220.01420.0640.15840.02450.242531.3386-16.292840.6312
60.3844-0.187-0.21491.5337-0.15980.8815-0.0225-0.0277-0.0422-0.0090.0026-0.162-0.0280.06450.01430.11330.00850.01460.1341-0.01210.205531.7774-16.009844.7886
70.18680.05690.14871.6102-0.49780.3629-0.1330.0433-0.16020.32510.0988-0.21410.16720.14910.00670.1966-0.01390.01160.1598-0.030.243130.6772-15.185247.125
80.0723-0.0381-0.13360.29380.31830.60150.13810.7219-0.1698-0.1078-0.26470.08030.28-0.20150.06690.54020.08170.32610.8463-0.28290.484939.1354-27.294323.3484
90.2703-0.26770.48740.90860.06340.9862-0.01930.1522-0.1536-0.0635-0.0030.3964-0.0407-0.29820.01380.1919-0.01050.01060.1763-0.00420.338624.5793-21.976438.8107
100.5346-0.1106-0.11810.42670.36870.5991-0.13790.3920.43550.31250.45630.3175-0.98980.3198-0.16450.7426-0.21240.04330.82390.1420.471649.94783.0273-8.1561
110.1568-0.37480.15420.9347-0.21520.84950.35760.5150.27490.31540.1290.05010.2560.2391-0.30420.6680.1793-0.11371.3369-0.45471.426752.7174-13.9108-7.8565
121.5360.89120.50731.00780.59370.6698-0.43920.7132-0.3195-0.1320.6285-0.0412-0.10960.3538-0.13770.60660.0457-0.00540.98810.13160.614652.8779-3.9031-8.1868
132.34740.2094-1.42050.73620.00582.03350.01410.19990.1606-0.19150.01560.0473-0.1693-0.0412-0.01290.2333-0.0204-0.00820.19530.04630.1481-3.80970.740917.2345
140.25240.3389-0.60211.9562-1.10791.9696-0.00240.3384-0.11860.17490.23330.5525-0.2585-0.4264-0.21990.0294-0.0101-0.01760.15860.02780.2135-22.3149-18.015942.331
150.8026-0.27120.20761.5313-0.1750.71760.12370.1478-0.0354-0.0343-0.0244-0.05310.02280.0997-0.08430.09190.0121-0.01010.1347-0.02640.194-6.4117-20.163940.5344
160.537-0.1963-0.02432.0143-0.45341.2105-0.0497-0.06440.02540.11490.0604-0.1422-0.02080.13430.00030.0933-0.0012-0.02130.1407-0.00360.1568-5.3846-19.108845.6463
170.2540.08910.05381.0540.13220.0693-0.14750.7405-0.27120.7115-0.34760.22860.17230.10850.21470.56820.34620.06750.6849-0.28970.45552.3099-31.489425.3286
180.67330.0795-0.31330.26170.09010.332-0.04840.0894-0.1798-0.04760.10180.26310.1726-0.1695-0.0040.12020.0135-0.00320.12310.02010.2456-14.4342-25.894842.8034
192.0917-0.3193-0.59471.8821.1180.95190.26970.7921-0.2244-0.65830.15430.07750.35160.4107-0.21760.47670.1326-0.00190.4265-0.05950.2693-4.0365-24.132424.0907
206.5862-1.38145.07913.6031-0.4134.10850.2312-0.3006-0.00440.5143-0.06240.0691-0.05820.59170.19920.9493-0.43850.06260.99930.19570.94727.0674-23.89310.7586
211.54670.0449-0.69510.6884-0.75831.3542-0.04280.0949-0.0444-0.18670.22510.1285-0.0023-0.2647-0.15020.3615-0.1624-0.04340.40850.06460.152513.8811-6.8342-8.9013
220.3668-0.0136-0.25720.8368-0.23120.5742-0.1345-0.19520.3382-0.2655-0.1949-0.3186-0.26960.20590.08960.3815-0.05140.03270.65460.080.291221.6220.2097-12.7608
230.6497-0.0079-0.26940.21790.28230.36990.07730.1586-0.1118-0.03890.14140.12630.28380.5869-0.11570.3553-0.0325-0.06880.57480.05840.223519.3236-5.6087-7.3481
240.0828-0.1498-0.04851.24530.21790.04090.71440.17190.1846-0.7476-0.5534-0.3180.291-0.0891-0.13210.5492-0.05070.12750.96370.08610.12819.281811.1372-32.8165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 236:271)
2X-RAY DIFFRACTION2(chain A and resid 272:302)
3X-RAY DIFFRACTION3(chain A and resid 303:343)
4X-RAY DIFFRACTION4(chain A and resid 344:400)
5X-RAY DIFFRACTION5(chain A and resid 401:434)
6X-RAY DIFFRACTION6(chain A and resid 435:498)
7X-RAY DIFFRACTION7(chain A and resid 499:517)
8X-RAY DIFFRACTION8(chain A and resid 518:523)
9X-RAY DIFFRACTION9(chain A and resid 524:550)
10X-RAY DIFFRACTION10(chain A and resid 558:587)
11X-RAY DIFFRACTION11(chain A and resid 588:593)
12X-RAY DIFFRACTION12(chain A and resid 594:673)
13X-RAY DIFFRACTION13(chain B and resid 235:382)
14X-RAY DIFFRACTION14(chain B and resid 383:393)
15X-RAY DIFFRACTION15(chain B and resid 394:436)
16X-RAY DIFFRACTION16(chain B and resid 437:516)
17X-RAY DIFFRACTION17(chain B and resid 517:523)
18X-RAY DIFFRACTION18(chain B and resid 524:544)
19X-RAY DIFFRACTION19(chain B and resid 545:550)
20X-RAY DIFFRACTION20(chain B and resid 551:560)
21X-RAY DIFFRACTION21(chain B and resid 561:627)
22X-RAY DIFFRACTION22(chain B and resid 628:645)
23X-RAY DIFFRACTION23(chain B and resid 646:672)
24X-RAY DIFFRACTION24(chain B and resid 673:679)

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