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- PDB-5tu8: Crystal structure of Staphylococcus epidermidis Aap G58-spacer-G5... -

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Basic information

Entry
Database: PDB / ID: 5tu8
TitleCrystal structure of Staphylococcus epidermidis Aap G58-spacer-G513* (variant G5-spacer-variant G5)
ComponentsAap G58-spacer-G513* (variant G5-spacer-variant G5)
KeywordsPROTEIN BINDING / biofilm intercellular adhesion Staphylococcus Aap
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsShelton, C.L. / Conrady, D.G. / Herr, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM094363 United States
American Heart Association13PRE16380011 United States
CitationJournal: Biochem. J. / Year: 2017
Title: Functional consequences of B-repeat sequence variation in the staphylococcal biofilm protein Aap: deciphering the assembly code.
Authors: Shelton, C.L. / Conrady, D.G. / Herr, A.B.
History
DepositionNov 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aap G58-spacer-G513* (variant G5-spacer-variant G5)
B: Aap G58-spacer-G513* (variant G5-spacer-variant G5)


Theoretical massNumber of molelcules
Total (without water)45,1662
Polymers45,1662
Non-polymers00
Water4,161231
1
A: Aap G58-spacer-G513* (variant G5-spacer-variant G5)


Theoretical massNumber of molelcules
Total (without water)22,5831
Polymers22,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aap G58-spacer-G513* (variant G5-spacer-variant G5)


Theoretical massNumber of molelcules
Total (without water)22,5831
Polymers22,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.623, 54.229, 184.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aap G58-spacer-G513* (variant G5-spacer-variant G5)


Mass: 22582.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 35984 / RP62A / Gene: aap, SERP2398 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q5HKE8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate pH 5 175 mM calcium chloride 22% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→92.25 Å / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.52 / % possible all: 89

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSNovember 3, 2014data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FUP

4fup


Resolution: 2.33→92.25 Å / Cor.coef. Fo:Fc: 0.9146 / Cor.coef. Fo:Fc free: 0.8903 / SU R Cruickshank DPI: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 984 5.14 %RANDOM
Rwork0.2099 ---
obs0.2117 19129 97.83 %-
Displacement parametersBiso mean: 50.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.8647 Å20 Å20 Å2
2--0.2035 Å20 Å2
3---1.6612 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: 1 / Resolution: 2.33→92.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 0 231 2230
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.232766HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d688SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it2037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
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_contact2310SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.46 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2505 138 5.39 %
Rwork0.2247 2420 -
all0.2261 2558 -
obs--97.83 %

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