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- PDB-1tf0: Crystal structure of the GA module complexed with human serum albumin -

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Basic information

Entry
Database: PDB / ID: 1tf0
TitleCrystal structure of the GA module complexed with human serum albumin
Components
  • Peptostreptococcal albumin-binding protein
  • Serum albumin
KeywordsPROTEIN BINDING / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Serum Albumin; Chain A, Domain 1 - #10 / GA-like domain / GA-like domain / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site ...Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Serum Albumin; Chain A, Domain 1 - #10 / GA-like domain / GA-like domain / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Immunoglobulin/albumin-binding domain superfamily / Serum Albumin; Chain A, Domain 1 / 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
CITRIC ACID / DECANOIC ACID / Albumin / Peptostreptococcal albumin-binding protein
Similarity search - Component
Biological speciesFinegoldia magna (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLejon, S. / Svensson, S. / Bjorck, L. / Frick, I.-M. / Wikstrom, M.
CitationJournal: 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
DepositionMay 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Peptostreptococcal albumin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9666
Polymers71,2572
Non-polymers7094
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.295, 134.799, 122.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serum albumin /


Mass: 65317.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue fraction: plasma / References: UniProt: P02768
#2: Protein Peptostreptococcal albumin-binding protein


Mass: 5939.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Gene: PAB / Plasmid: pHD389 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q51911
#3: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H20O2
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2003 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 24858 / Num. obs: 24858 / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
ProDCdata collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1AO6 and 1PRB

1ao6

1prb


Resolution: 2.7→65 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.879 / SU B: 31.497 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.22 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29497 1103 5 %RANDOM
Rwork0.24886 ---
obs0.25113 21137 100 %-
all-22263 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.306 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2---1.22 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 49 0 4902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225005
X-RAY DIFFRACTIONr_bond_other_d0.0010.024479
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9726749
X-RAY DIFFRACTIONr_angle_other_deg0.913310528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8025606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19325.127236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28415916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8551523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
X-RAY DIFFRACTIONr_nbd_refined0.2570.21489
X-RAY DIFFRACTIONr_nbd_other0.1920.24766
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.23053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.53263
X-RAY DIFFRACTIONr_mcbond_other0.1191.51209
X-RAY DIFFRACTIONr_mcangle_it1.04524920
X-RAY DIFFRACTIONr_scbond_it1.58532117
X-RAY DIFFRACTIONr_scangle_it2.474.51829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 79
Rwork0.324 1543
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)
13.369-0.6051-0.07865.0671-0.27422.96390.22190.946-0.0341-1.0512-0.2668-0.3276-0.54090.28740.04490.5257-0.1170.19540.46020.03740.357631.55876.67413.533
22.98770.0776-1.0392.54660.02014.62430.0732-0.0777-0.0768-0.11840.0499-0.3321-0.2850.3423-0.1231-0.0911-0.00430.0257-0.0705-0.04250.031217.60669.21241.418
33.1385-1.8274-0.57234.79721.37394.40120.05750.1388-0.0835-0.3134-0.1591-0.15870.61240.25890.1016-0.01490.06970.05810.132-0.00210.200722.38145.31918.656
410.34172.62170.73226.757-0.79694.03910.2742-0.10120.54060.0998-0.0680.1423-1.29750.0532-0.20620.3990.00030.1624-0.0666-0.003-0.036313.70685.62249.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1975 - 197
2X-RAY DIFFRACTION2AA198 - 385198 - 385
3X-RAY DIFFRACTION3AA386 - 569386 - 569
4X-RAY DIFFRACTION4BB1 - 531 - 53

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