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- PDB-4fum: Structural basis for Zn2+-dependent intercellular adhesion in sta... -

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Basic information

Entry
Database: PDB / ID: 4fum
TitleStructural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms
ComponentsAccumulation associated protein
KeywordsMEMBRANE PROTEIN / hydrophilic protein / non-globular / freestanding beta sheet / intercellular adhesion / zinc dependent dimer
Function / homology
Function and homology information


Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / Bacterial lectin / 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 / Bacterial lectin / 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 / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsConrady, D.G. / Wilson, J.J. / Herr, A.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms.
Authors: Conrady, D.G. / Wilson, J.J. / Herr, A.B.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6963
Polymers22,5721
Non-polymers1232
Water1,13563
1
A: Accumulation associated protein
hetero molecules

A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3926
Polymers45,1452
Non-polymers2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3370 Å2
ΔGint-87 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.721, 33.637, 81.325
Angle α, β, γ (deg.)90.000, 121.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Accumulation associated protein


Mass: 22572.314 Da / Num. of mol.: 1 / Fragment: UNP residues 2017-2223 / Mutation: L24M, L51M, L152M, L179M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: RP62A / Gene: aap, SERP2398 / Plasmid: pH596 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q5HKE8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: batch / pH: 7.9
Details: 0.12 M Postassium Thiocyanate, 0.1 M Tris pH 7.9, 28% PEG MME 2000, 3% Ethanol, batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2010
RadiationProtocol: SINGLE WAVELENGTH, INVERSE BEAM / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8282 / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.111

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutosolphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.4→44.82 Å / Cor.coef. Fo:Fc: 0.9206 / Cor.coef. Fo:Fc free: 0.9048 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 382 4.61 %RANDOM
Rwork0.1979 ---
obs0.2006 8278 --
Displacement parametersBiso max: 147.59 Å2 / Biso mean: 64.3722 Å2 / Biso min: 27.23 Å2
Baniso -1Baniso -2Baniso -3
1--7.4612 Å20 Å29.4281 Å2
2---7.5103 Å20 Å2
3---14.9715 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 4 63 1547
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6762
X-RAY DIFFRACTIONt_trig_c_planes382
X-RAY DIFFRACTIONt_gen_planes2155
X-RAY DIFFRACTIONt_it151620
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2195
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15314
X-RAY DIFFRACTIONt_bond_d151620.009
X-RAY DIFFRACTIONt_angle_deg206821.2
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion2.93
LS refinement shellResolution: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3015 96 4.2 %
Rwork0.2108 2190 -
all0.2145 2286 -
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)
1-7.7696-2.05252.5867.09048.437612.83140.07980.34160.1785-0.19950.15840.1782-0.0664-0.4405-0.23820.2498-0.3303-0.28760.40250.24720.0949-2.507616.9672-51.3337
21.6344.5904-1.47154.66550.37510.7732-0.29240.38260.272-0.98090.33410.07180.06820.0616-0.0417-0.19910.0558-0.0837-0.15030.0446-0.326314.286715.0491-31.3254
36.63648.64234.38916.26098.961615.9729-0.335-0.92440.22831.18490.28320.3701-0.30550.67260.0519-0.19590.0516-0.013-0.31020.0011-0.310218.996414.5119-13.9019
44.6993-0.55572.43560.0319-0.31541.8108-0.39490.77590.1627-0.31520.1057-0.0568-0.29750.10950.28920.0747-0.2477-0.2393-0.33140.0302-0.28151.978316.7895-43.2347
5-8.0384-4.1242.707212.5724-4.664113.1699-0.05680.3445-0.3587-0.4235-0.317-0.06410.0690.19470.37380.4328-0.2485-0.37120.7053-0.18350.355-4.126518.8629-63.7071
611.28541.8012.166912.9692-7.1838-1.4835-0.1064-0.29040.178-0.16640.0264-0.0259-0.2734-0.18440.080.1529-0.0905-0.1310.0135-0.0095-0.02961.590321.7335-40.1337
7-1.7306-1.8113-0.02122.9771-1.62529.8194-0.14780.07770.43250.15130.1606-0.0433-0.13981.1527-0.01280.0426-0.0664-0.1243-0.1348-0.0168-0.171117.320114.7846-20.1974
83.7091-3.07735.73690.989-2.74175.56510.09240.0919-0.2661-0.13490.15570.39680.98730.1277-0.24810.0306-0.0577-0.0322-0.23380.0319-0.129728.369216.367217.4337
91.26761.86176.42873.59020.818810.273-0.16380.4721-0.10890.0830.1568-0.16590.3323-0.37510.007-0.06470.0981-0.1150.01220.0243-0.155725.593716.6678-2.2465
10-0.09870.56366.32620.3061-0.84788.9285-0.37510.41510.0996-0.06340.2419-0.1645-0.20760.40290.13320.15610.0396-0.12070.0692-0.00730.009127.961219.51571.3204
111.2313-0.34894.34630-1.637624.38930.344-0.0017-0.125-0.03150.1581-0.0945-0.03361.2134-0.50210.0770.0482-0.004-0.0265-0.0013-0.170937.571417.143347.9502
125.54230.79693.998611.4667-10.598616.2289-0.17160.3998-0.1276-0.623-0.15030.00570.05460.96450.32190.06790.0531-0.0928-0.3142-0.0739-0.201739.538323.638288.7184
136.6473-1.08522.00810.3177-5.48391.9066-0.2531-0.24360.00380.65560.012-0.39810.32140.26960.24110.36150.2023-0.0621-0.0046-0.0726-0.183841.416616.142381.0735
14-4.0966-0.1363-1.316401.548415.70490.0274-0.21180.15990.0208-0.18180.1037-0.09110.21990.15430.24070.0325-0.02470.18550.0237-0.146536.734917.193551.8944
152.46480.97465.88291.0434-5.194715.62780.2145-0.1477-0.21030.91040.33920.0117-0.084-0.1521-0.55370.04830.0238-0.0392-0.25910.0311-0.181835.549119.051931.5114
16-0.20050.63980.426303.914118.33020.22170.5856-0.1174-0.1137-0.0316-0.19090.3269-0.2571-0.19010.2890.0813-0.04880.1813-0.0233-0.111937.093219.216170.8273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 11}A2 - 11
2X-RAY DIFFRACTION2{A|12 - 18}A12 - 18
3X-RAY DIFFRACTION3{A|19 - 30}A19 - 30
4X-RAY DIFFRACTION4{A|31 - 49}A31 - 49
5X-RAY DIFFRACTION5{A|50 - 62}A50 - 62
6X-RAY DIFFRACTION6{A|63 - 68}A63 - 68
7X-RAY DIFFRACTION7{A|69 - 80}A69 - 80
8X-RAY DIFFRACTION8{A|81 - 99}A81 - 99
9X-RAY DIFFRACTION9{A|100 - 111}A100 - 111
10X-RAY DIFFRACTION10{A|112 - 125}A112 - 125
11X-RAY DIFFRACTION11{A|126 - 144}A126 - 144
12X-RAY DIFFRACTION12{A|145 - 156}A145 - 156
13X-RAY DIFFRACTION13{A|157 - 162}A157 - 162
14X-RAY DIFFRACTION14{A|163 - 175}A163 - 175
15X-RAY DIFFRACTION15{A|176 - 188}A176 - 188
16X-RAY DIFFRACTION16{A|189 - 207}A189 - 207

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