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- PDB-2j5y: Crystal structure of the GA module from F.magna -

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Basic information

Entry
Database: PDB / ID: 2j5y
TitleCrystal structure of the GA module from F.magna
ComponentsPEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
KeywordsPROTEIN BINDING / CELL WALL / PEPTIDOGLYCAN-ANCHOR / PROTEIN BINDING BACTERIAL ALBUMIN-BINDING THREE-HELIX BUNDLE
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 ...Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptostreptococcal albumin-binding protein
Similarity search - Component
Biological speciesPEPTOSTREPTOCOCCUS MAGNUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLejon, S. / Cramer, J.F. / Nordberg, P.A. / Lundqvist, T. / Valegard, K.
Citation
Journal: FEBS Lett. / Year: 2007
Title: Crystal Structure of a Bacterial Albumin-Binding Domain at 1.4A Resolution.
Authors: Cramer, J.F. / Nordberg, P.A. / Hajdu, J. / Lejon, S.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure and Biological Implications of a Bacterial Albumin-Binding Module in Complex with Human Serum Albumin
Authors: Lejon, S. / Frick, I.-M. / Bjorck, L. / Wikstrom, M. / Svensson, S.
History
DepositionSep 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
B: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,6402
Polymers13,6402
Non-polymers00
Water3,297183
1
A: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,8201
Polymers6,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,8201
Polymers6,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)25.784, 58.068, 40.570
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: -7 - 53 / Label seq-ID: 1 - 61

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

NCS oper: (Code: given
Matrix: (-1, 0.00041, -0.0006), (-0.00041, -1, -0.00038), (-0.0006, -0.00038, 1)
Vector: 12.89728, 1.58441, 20.28773)

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Components

#1: Protein PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN / GA MODULE


Mass: 6819.855 Da / Num. of mol.: 2 / Fragment: ALBUMIN-BINDING DOMAIN, RESIDUES 213-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PEPTOSTREPTOCOCCUS MAGNUS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51911
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGA DOMAIN OF PROTEIN PAB, SPANNING AMINO ACIDS 213-265.

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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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growpH: 7.5
Details: 22-26% (W/V) PEG 3350, 50 MM POTASSIUM PHOSPHATE PH 7.5, 100 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2005 / Details: PT-COATED MIRRORS IN KB GEOMETRY
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 22273 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.8 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TF0, CHAIN B

1tf0


Resolution: 1.4→40.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.055 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DISORDERED SIDE CHAINS HAVE BEEN MODELLED WITH ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1152 5.2 %RANDOM
Rwork0.148 ---
obs0.151 21101 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.03 Å2
2---0.32 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 0 183 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9281443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9635144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00225.91849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5815191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.325152
X-RAY DIFFRACTIONr_chiral_restr0.1240.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02798
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2745
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8681.5670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.74921062
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0173424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5454.5370
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
237tight positional0.070.05
230medium positional0.370.5
237tight thermal0.470.5
230medium thermal1.52
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 45
Rwork0.189 1100

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