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- PDB-4f5u: Crystal structure of Equine Serum Albumin at 2.04 resolution -

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Basic information

Entry
Database: PDB / ID: 4f5u
TitleCrystal structure of Equine Serum Albumin at 2.04 resolution
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Equine serum albumin / helical protein
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / MALONATE ION / SUCCINIC ACID / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBujacz, A. / Bujacz, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of bovine, equine and leporine serum albumin.
Authors: Bujacz, A.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7199
Polymers65,8541
Non-polymers8648
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.254, 89.254, 134.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serum albumin /


Mass: 65854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80% Tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2011 / Details: mirrors
RadiationMonochromator: Double crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 38668 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.7
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5T

4f5t


Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.617 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24294 1211 3.1 %RANDOM
Rwork0.19612 ---
obs0.19756 37399 99.84 %-
all-38668 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.582 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20.99 Å20 Å2
2--1.99 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 59 345 5013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.9916538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89725222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73515879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4271522
X-RAY DIFFRACTIONr_chiral_restr0.110.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213664
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8251.52954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44524767
X-RAY DIFFRACTIONr_scbond_it2.55731879
X-RAY DIFFRACTIONr_scangle_it3.9464.51762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 87 -
Rwork0.33 2732 -
obs--98.84 %
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)
11.71280.48470.05582.82610.75321.21410.11360.11620.0810.12310.0230.28610.0048-0.2314-0.13650.18820.0868-0.02880.11810.01120.1958-15.050153.917968.1691
21.94710.0291-0.6494.9162-0.48390.59320.11850.35620.2362-0.6181-0.1101-0.1338-0.1107-0.0467-0.00840.32840.117-0.03480.20820.0010.18210.11454.259154.8582
31.23320.2424-0.03644.2911-1.77260.98610.18290.25970.1303-0.2551-0.2971-0.4159-0.18580.25760.11430.4742-0.010.07250.23580.01310.25998.528653.986760.8865
41.5765-1.2426-0.09893.17831.25932.2516-0.108-0.0887-0.0320.1908-0.01620.3525-0.0443-0.02880.12420.07560.01010.01150.0439-0.03790.07293.358942.448380.4591
53.5863-1.76710.35883.16750.06563.01280.1066-0.07640.2755-0.0815-0.0372-0.2432-0.470.184-0.06940.2105-0.04740.01810.0436-0.0590.13659.466154.91580.3783
61.43411.49870.48727.9697-0.56692.7238-0.0423-0.2488-0.17950.7194-0.04890.04810.08340.07180.09110.19690.06490.03040.2384-0.02580.143813.395632.482992.9386
72.67091.34910.03062.13-2.20527.25340.083-0.2131-0.30320.10960.02430.16360.5016-0.3162-0.10730.16580.0460.04280.1244-0.01340.186812.22625.579485.6224
82.31212.7094-5.26833.6303-8.722926.4313-0.2011-0.1182-0.3995-0.1782-0.2499-0.37290.28450.7740.4510.1950.14720.06910.22310.03360.342221.133826.36574.2207
96.49970.6246-0.8591.81140.53392.118-0.11580.08250.0046-0.06410.0816-0.0050.08670.28420.03430.05150.04910.00530.0982-0.01380.028513.125228.297854.6325
102.09140.25551.37151.10621.15773.52550.02470.04930.0349-0.0411-0.0153-0.0679-0.13150.2329-0.00940.06350.01040.00910.054-0.02260.078510.568435.233462.3075
112.66031.15510.44835.8021.59885.13-0.1421-0.0065-0.22390.24190.11130.16820.75090.05920.03070.14330.03980.03890.0757-0.00690.10685.211422.339764.3905
122.79691.1241-0.15313.3264-2.61264.8181-0.00230.34550.06660.15780.02370.08840.0219-0.0809-0.02140.07890.06610.01330.1932-0.02870.09369.424830.507742.2878
131.59770.02870.82462.8404-1.45453.32650.06280.38960.0721-0.0502-0.0841-0.02850.07980.40180.02130.04020.07830.02320.262-0.02050.103417.104128.370736.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 583

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