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- PDB-8pxc: Structure of Fap1, a domain of the accessory Sec-dependent serine... -

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Basic information

Entry
Database: PDB / ID: 8pxc
TitleStructure of Fap1, a domain of the accessory Sec-dependent serine-rich glycoprotein adhesin from Streptococcus oralis, solved at wavelength 3.06 A
ComponentsFap1
KeywordsCELL ADHESION / Sec-dependent serine-rich glycoprotein adhesin
Biological speciesStreptococcus oralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Owen, C.D. / Walsh, M.A. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7737
Polymers48,4441
Non-polymers3286
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.810, 30.400, 90.600
Angle α, β, γ (deg.)90.00, 127.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fap1


Mass: 48444.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus oralis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.51 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-Tris 5.5 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.066 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.066 Å / Relative weight: 1
ReflectionResolution: 1.973→65.53 Å / Num. obs: 17626 / % possible obs: 84.33 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1122 / Rpim(I) all: 0.03096 / Rrim(I) all: 0.1169 / Net I/σ(I): 20.29
Reflection shellResolution: 1.973→2.043 Å / Mean I/σ(I) obs: 8.67 / Num. unique obs: 1321 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.973→65.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.059 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22042 900 5.1 %RANDOM
Rwork0.1812 ---
obs0.18316 16726 84.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.941 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.41 Å2
2---1.36 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.973→65.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 18 259 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161830
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6672718
X-RAY DIFFRACTIONr_angle_other_deg0.4861.5614223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.22958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14410305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9330.7891026
X-RAY DIFFRACTIONr_mcbond_other0.9330.7891026
X-RAY DIFFRACTIONr_mcangle_it1.5821.4041282
X-RAY DIFFRACTIONr_mcangle_other1.5821.4081283
X-RAY DIFFRACTIONr_scbond_it1.5640.969974
X-RAY DIFFRACTIONr_scbond_other1.5640.97975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.491.6921434
X-RAY DIFFRACTIONr_long_range_B_refined10.81911.438901
X-RAY DIFFRACTIONr_long_range_B_other10.81310.598677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.973→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 53 -
Rwork0.221 884 -
obs--60.61 %
Refinement TLS params.Method: refined / Origin x: 27.3998 Å / Origin y: -6.1218 Å / Origin z: 26.9192 Å
111213212223313233
T0.0032 Å2-0.0064 Å2-0.0125 Å2-0.079 Å20.0076 Å2--0.0778 Å2
L0.238 °2-0.1566 °2-0.3142 °2-0.3882 °20.3561 °2--1.3442 °2
S-0.0012 Å °-0.0352 Å °0.0209 Å °0.0182 Å °0.0331 Å °-0.0317 Å °0.0062 Å °0.0546 Å °-0.0318 Å °

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