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- PDB-7q4x: Crystal Structure of Equine Serum Albumin in Complex with Cefaclor -

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Basic information

Entry
Database: PDB / ID: 7q4x
TitleCrystal Structure of Equine Serum Albumin in Complex with Cefaclor
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / antibiotic transport / cefaclor binding / complex
Function / homology
Function and homology information


lipid binding / extracellular space / metal ion binding
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
Cefaclor / ACETATE ION / FORMIC ACID / (2S)-2-hydroxybutanedioic acid / MALONATE ION / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDuszynski, K. / Sekula, B. / Bujacz, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/11/B/ST5/02271 Poland
CitationJournal: To Be Published
Title: Binding of beta-lactam antibiotics by equine, caprine and ovine serum albumins
Authors: Sekula, B. / Duszynski, K. / Talaj, J. / Bujacz, A.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,09218
Polymers65,2721
Non-polymers1,82017
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint12 kcal/mol
Surface area26190 Å2
Unit cell
Length a, b, c (Å)94.750, 94.750, 142.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Albumin


Mass: 65271.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: Blood / References: UniProt: F7BAY6

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Non-polymers , 6 types, 156 molecules

#2: Chemical ChemComp-8XI / Cefaclor / (6R,7R)-7-[[(2R)-2-azanyl-2-phenyl-ethanoyl]amino]-3-chloranyl-8-oxidanylidene-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid


Mass: 367.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14ClN3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Native ESA crystals grown in 2.0 M ammonium sulfate and 0.1 M acetate buffer at pH 5.0 soaked with cefaclor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 / Details: Sagittally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.12→47.38 Å / Num. obs: 41089 / % possible obs: 99.8 % / Redundancy: 13.81 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 1 / Net I/σ(I): 22.27
Reflection shellResolution: 2.12→2.49 Å / Redundancy: 13.97 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 6556 / CC1/2: 0.597 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDS2data reduction
Coot0.8.1model building
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZBQ

4zbq


Resolution: 2.12→47.38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.181 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2052 5 %RANDOM
Rwork0.1866 ---
obs0.1897 38982 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.47 Å2 / Biso mean: 57.168 Å2 / Biso min: 29.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 2.12→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 121 139 4828
Biso mean--74.6 53.13 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194824
X-RAY DIFFRACTIONr_angle_refined_deg2.5251.9656509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38624.93213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12215866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1781521
X-RAY DIFFRACTIONr_chiral_restr0.1590.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213641
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 151 -
Rwork0.331 2868 -
all-3019 -
obs--99.74 %
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)
15.0098-0.9710.54451.22080.32691.19560.14390.17280.1139-0.37620.11930.1056-0.1629-0.163-0.26320.2603-0.1001-0.03050.13990.12290.141841.691542.265370.8029
28.4692-2.0627-4.01872.1720.46983.45710.35370.7061-0.0692-0.6439-0.0773-0.45260.28310.12-0.27640.5861-0.1153-0.07270.3675-0.10240.334650.606828.95657.632
35.95860.38-3.00082.5969-0.76483.0420.08050.2108-0.5083-0.7022-0.1375-0.52720.16950.49170.0570.3684-0.08840.04650.3976-0.04630.236354.854121.287363.6932
41.18681.15451.17791.6990.72711.47680.0578-0.00020.22640.0963-0.16130.36460.05810.11940.10350.1508-0.0039-0.0660.1164-0.02090.137641.122319.819484.5748
51.41091.76730.70253.3098-0.06671.3077-0.0630.2396-0.16590.00420.1687-0.2984-0.09180.425-0.10570.0747-0.0414-0.04780.3403-0.13380.125355.650120.723284.5115
65.24090.71680.03080.1563-0.00840.00570.0996-0.39520.16120.144-0.1034-0.0151-0.01690.02550.00380.3314-0.0466-0.09030.17780.00020.031537.37135.131498.0146
72.3017-1.06070.03471.24990.60712.9972-0.1329-0.0736-0.14560.06970.11720.22360.0176-0.27480.01570.16920.0205-0.05590.1006-0.00160.104930.43962.536190.5514
81.2129-0.3435-2.49720.16990.36637.867-0.14590.0499-0.24370.0304-0.08530.09040.13350.0610.23110.2006-0.00480.01510.0966-0.00340.114636.0832-5.140578.0893
92.1912-2.17520.43952.5645-0.32130.2202-0.05870.09480.19940.0248-0.0661-0.11980.0378-0.08660.12480.2412-0.0192-0.00610.1487-0.05870.069933.3112.973457.6171
100.2557-0.12720.34520.74640.28760.81890.0015-0.03020.0261-0.11390.061-0.09560.02140.0249-0.06250.201-0.0061-0.0520.14160.00220.071938.61268.643465.8989
111.3848-1.5853-0.07912.0019-0.69755.4680.09080.0894-0.0698-0.1114-0.08970.18290.3848-0.5552-0.00110.1533-0.0758-0.00070.1676-0.0710.206523.97567.230167.9655
121.502-0.0132-1.2691.0085-1.37243.01060.15450.05450.0928-0.1593-0.1068-0.02530.00210.018-0.04770.3040.08180.00730.1145-0.02130.016733.30797.073544.7349
133.07231.949-1.34861.5546-1.5892.3491-0.00820.0727-0.0843-0.16550.0201-0.03890.2742-0.051-0.01190.30040.10280.01170.0756-0.00790.042135.0268-0.941938.6535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 109
2X-RAY DIFFRACTION2A110 - 150
3X-RAY DIFFRACTION3A151 - 201
4X-RAY DIFFRACTION4A202 - 253
5X-RAY DIFFRACTION5A254 - 298
6X-RAY DIFFRACTION6A299 - 339
7X-RAY DIFFRACTION7A340 - 369
8X-RAY DIFFRACTION8A370 - 401
9X-RAY DIFFRACTION9A402 - 420
10X-RAY DIFFRACTION10A421 - 471
11X-RAY DIFFRACTION11A472 - 500
12X-RAY DIFFRACTION12A501 - 540
13X-RAY DIFFRACTION13A541 - 583

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