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

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Basic information

Entry
Database: PDB / ID: 4fup
TitleStructural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms
ComponentsAccumulation associated protein
KeywordsMEMBRANE PROTEIN / hydrophilic protein / non-globular / freestanding beta sheet / 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
Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 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
Revision 1.2Feb 28, 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_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9004
Polymers44,7692
Non-polymers1312
Water1,946108
1
A: Accumulation associated protein
hetero molecules

A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9004
Polymers44,7692
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3700 Å2
ΔGint-84 kcal/mol
Surface area23660 Å2
MethodPISA
2
B: Accumulation associated protein
hetero molecules

B: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9004
Polymers44,7692
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3050 Å2
ΔGint-86 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.101, 34.240, 138.779
Angle α, β, γ (deg.)90.000, 101.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Accumulation associated protein


Mass: 22384.734 Da / Num. of mol.: 2 / Fragment: UNP residues 2017-2223 / Mutation: L24M, L51M, L152M, L179M
Source method: isolated from a genetically manipulated source
Details: point mutations L24M,L51M,L152M,L179M were generated using pcr site-directed mutagenesis
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: batch / pH: 7.9
Details: 0.12 M Postassium Thiocyanate, 0.1 M Tris pH7.9, 28% PEG MME 2000, 0.5% beta-octylglucopyranoside, 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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13488 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Χ2: 2.094 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.70.212972.135199.7
2.59-2.693.70.17313452.0461100
2.69-2.823.70.14413682.014199.9
2.82-2.963.70.11413352.2271100
2.96-3.153.70.09413392.18199.9
3.15-3.393.70.07913472.202199.8
3.39-3.733.70.07213662.285199.9
3.73-4.273.60.06613362.14199.1
4.27-5.383.50.06513461.797197.9
5.38-503.40.05714091.895197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→45.36 Å / Cor.coef. Fo:Fc: 0.8726 / Cor.coef. Fo:Fc free: 0.8337 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 662 4.93 %RANDOM
Rwork0.2192 ---
obs0.2219 13426 --
Displacement parametersBiso max: 101.68 Å2 / Biso mean: 32.5445 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--2.2319 Å20 Å2-5.8969 Å2
2---13.54 Å20 Å2
3---15.7719 Å2
Refine analyzeLuzzati coordinate error obs: 0.366 Å
Refinement stepCycle: LAST / Resolution: 2.51→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 2 108 2933
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1276SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes414HARMONIC5
X-RAY DIFFRACTIONt_it2889HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion419SEMIHARMONIC5
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_contact3128SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2889HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3954HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion2.82
LS refinement shellResolution: 2.51→2.71 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3577 156 5.77 %
Rwork0.2611 2548 -
all0.2668 2704 -

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