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- PDB-8deo: Structure of AAP A domain and B-repeats (residues 351-813) from S... -

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Basic information

Entry
Database: PDB / ID: 8deo
TitleStructure of AAP A domain and B-repeats (residues 351-813) from Staphylococcus epidermidis
ComponentsAccumulation associated protein
KeywordsCELL ADHESION / L-type lectin / Staphylococcus epidermidis
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / G5 domain / G5 domain / G5 domain profile. / G5 / : / YSIRK type signal peptide ...Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / G5 domain / G5 domain / G5 domain profile. / G5 / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single Sheet / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHarris, G. / Whelan, F. / Clark, L. / Turkenburg, J.P. / Potts, J.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005029/ United Kingdom
British Heart FoundationFS/12/36/29588 United Kingdom
British Heart FoundationPG/17/19/32862 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface.
Authors: Clark, L.C. / Atkin, K.E. / Whelan, F. / Brentnall, A.S. / Harris, G. / Towell, A.M. / Turkenburg, J.P. / Liu, Y. / Feizi, T. / Griffiths, S.C. / Geoghegan, J.A. / Potts, J.R.
History
DepositionJun 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Accumulation associated protein
B: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4916
Polymers101,3402
Non-polymers1514
Water3,027168
1
A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7463
Polymers50,6701
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7463
Polymers50,6701
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.482, 66.565, 66.873
Angle α, β, γ (deg.)84.695, 80.489, 89.664
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 352 - 813 / Label seq-ID: 6 - 467

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Accumulation associated protein


Mass: 50670.117 Da / Num. of mol.: 2 / Fragment: residues 351-813
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria)
Strain: ATCC 35984 / RP62A / Gene: aap, SERP2398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HKE8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 550 MME, 10% PEG 20K, 100 mM MOPS/HEPES pH 7 (Morpheus Buffer System 2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→39.709 Å / Num. obs: 42896 / % possible obs: 97.5 % / Redundancy: 2.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.08 / Rrim(I) all: 0.113 / Net I/σ(I): 4.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4169 / CC1/2: 0.764 / Rpim(I) all: 0.586 / Rrim(I) all: 0.829 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SIE

7sie


Resolution: 2.3→39.709 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.204 / SU B: 19.63 / SU ML: 0.226 / Average fsc free: 0.9524 / Average fsc work: 0.9615 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2120 4.942 %RANDOM
Rwork0.1975 40775 --
all0.2 ---
obs-42895 97.517 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.537 Å2
Baniso -1Baniso -2Baniso -3
1--3.365 Å20.378 Å20.289 Å2
2---2.534 Å2-1.177 Å2
3---5.386 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6692 0 4 168 6864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0116871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165790
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0560.147566
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6729355
X-RAY DIFFRACTIONr_angle_other_deg0.4921.56513604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2641023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05810991
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.40810304
X-RAY DIFFRACTIONr_chiral_restr0.0640.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021263
X-RAY DIFFRACTIONr_nbd_refined0.1910.21033
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.25086
X-RAY DIFFRACTIONr_nbtor_refined0.170.23279
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2221
X-RAY DIFFRACTIONr_metal_ion_refined0.20.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.237
X-RAY DIFFRACTIONr_nbd_other0.180.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.220
X-RAY DIFFRACTIONr_mcbond_it2.2662.9193637
X-RAY DIFFRACTIONr_mcbond_other2.2662.923636
X-RAY DIFFRACTIONr_mcangle_it3.5894.3734539
X-RAY DIFFRACTIONr_mcangle_other3.5894.3734540
X-RAY DIFFRACTIONr_scbond_it2.3842.9663234
X-RAY DIFFRACTIONr_scbond_other2.3842.9663235
X-RAY DIFFRACTIONr_scangle_it3.6494.4044815
X-RAY DIFFRACTIONr_scangle_other3.6494.4034816
X-RAY DIFFRACTIONr_lrange_it6.82999.23551677
X-RAY DIFFRACTIONr_lrange_other6.82999.24851663
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.0513062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.066350.05009
12AX-RAY DIFFRACTIONLocal ncs0.066350.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.3131540.32629880.32532480.8960.90296.73650.324
2.36-2.4240.31460.29428900.29431230.9340.9397.21420.289
2.424-2.4940.2851520.27628390.27630680.9440.93897.49020.27
2.494-2.570.3111270.2728140.27230220.9260.94697.31970.268
2.57-2.6540.2781470.23926780.24129070.9540.9697.17920.232
2.654-2.7470.2541250.22425800.22627690.9610.96197.68870.217
2.747-2.850.2611250.22925080.23127090.9520.96597.19450.22
2.85-2.9660.2671510.2123820.21325990.9560.97197.46060.202
2.966-3.0970.2531310.20423310.20625210.9550.97597.65970.198
3.097-3.2470.248970.19422290.19623780.960.97797.81330.19
3.247-3.4220.2451170.20121200.20322820.9610.97898.0280.197
3.422-3.6280.2551000.219930.20321410.9630.97797.75810.202
3.628-3.8760.2531000.18119020.18520420.9630.98198.04110.184
3.876-4.1830.1971010.15217550.15518840.9780.98398.51380.159
4.183-4.5770.188830.13815810.1416990.9820.98997.940.154
4.577-5.1090.172830.1414640.14215820.9860.98897.78760.161
5.109-5.8830.255540.17612980.17913770.9670.98298.18450.203
5.883-7.1660.3470.19510980.19811770.9540.97797.28120.221
7.166-9.9730.216610.1828310.1849210.9720.97996.85120.211
9.973-39.7090.252190.1884930.195280.9620.97796.96970.227
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)
12.34110.1212-0.10673.07570.22661.75890.12430.0694-0.1540.0228-0.0860.02470.1495-0.0188-0.03830.13880.0044-0.07350.005-0.00890.0673-35.677513.19515.988
28.6018-2.9361.75651.3148-0.6740.37650.06610.56480.1923-0.0657-0.1401-0.19820.01770.09820.0740.59640.1220.01840.8258-0.08370.847417.1122-8.5072-9.4604
33.8307-3.35151.1654.9531-1.0652.20170.03210.04040.23070.123-0.06471.0318-0.297-0.93010.03250.28280.13190.00960.4846-0.00270.799966.9067-23.9877-10.4412
46.5902-3.3377-1.16271.71020.5950.20790.04120.05520.5402-0.02940.0656-0.2684-0.00260.0231-0.10680.3790.06610.05310.4634-0.00680.4186115.7852-44.949-12.9768
52.09090.0528-0.06473.2448-0.23521.76470.0765-0.0488-0.1288-0.0411-0.07780.08470.14980.06850.00130.1125-0.0239-0.04380.0298-0.0140.068224.416846.570621.8197
68.09511.5712-0.34382.6683-0.00811.68090.02120.0072-0.3312-0.0786-0.0570.35830.1254-0.17960.03580.42110.0013-0.01290.40870.0780.4592-38.552320.134636.6455
76.60842.37510.16260.92360.05850.03240.2864-0.41670.59730.1111-0.25840.02930.00240.1012-0.0280.3287-0.1137-0.01690.6390.09240.605-53.156517.781137.458
89.24054.6745-0.95682.3755-0.47740.11080.3007-0.3963-0.02070.2068-0.2253-0.0483-0.03040.0118-0.07540.3744-0.09320.01960.49260.06560.437-128.6744-12.826140.6342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA351 - 612
2X-RAY DIFFRACTION2ALLA613 - 685
3X-RAY DIFFRACTION3ALLA686 - 737
4X-RAY DIFFRACTION4ALLA738 - 813

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