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- PDB-5otb: Structure of caprine serum albumin in P1 space group -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5otb
TitleStructure of caprine serum albumin in P1 space group
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / caprine serum albumin / goat serum albumin / P1
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PROLINE / Albumin
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTalaj, J.A. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2013/11/B/ST5/02271 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structures of serum albumins from domesticated ruminants and their complexes with 3,5-diiodosalicylic acid.
Authors: Bujacz, A. / Talaj, J.A. / Zielinski, K. / Pietrzyk-Brzezinska, A.J. / Neumann, P.
History
DepositionAug 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Albumin
C: Albumin
D: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,58020
Polymers265,6514
Non-polymers1,92916
Water8,683482
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7934
Polymers66,4131
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7934
Polymers66,4131
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0146
Polymers66,4131
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9796
Polymers66,4131
Non-polymers5675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.750, 80.930, 110.530
Angle α, β, γ (deg.)90.01, 75.90, 72.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Albumin / / Caprine serum albumin


Mass: 66412.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Plasmid details: serum plasma / Tissue: Blood / References: UniProt: B3VHM9
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.44 Å3/Da / Density % sol: 49.61 % / Description: plate
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0,2M L-Proline, Hepes pH 7,5, 24% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2013 / Details: mirrors
RadiationMonochromator: S 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 85355 / % possible obs: 98.1 % / Redundancy: 3.15 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.97
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 9218 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ORI
Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.529 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.82 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24595 1708 2 %RANDOM
Rwork0.19749 ---
obs0.19845 83645 98.15 %-
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: 64.673 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å2-0.29 Å2-1.21 Å2
2---0.27 Å2-0.57 Å2
3----3.12 Å2
Refinement stepCycle: 1 / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18511 0 132 482 19125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01919097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9825800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65352322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7224.955880
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.49153488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9771588
X-RAY DIFFRACTIONr_chiral_restr0.1330.22832
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114232
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_it5.3124.5659326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.786.82911631
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2224.8359771
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.34538.57830544
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 121 -
Rwork0.273 5886 -
obs--93.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.00860.06510.92680.49170.57561.0461-0.00840.19220.1038-0.1110.1402-0.1684-0.1050.2108-0.13180.142-0.0010.02690.1898-0.04990.237774.470228.454142.5451
20.07760.0580.39870.05330.26122.2334-0.0038-0.0104-0.0294-0.0227-0.0333-0.05120.0323-0.02870.03710.15520.0553-0.01240.1515-0.0220.234855.224822.057837.4729
31.5270.79680.56461.55460.32620.39120.0836-0.0450.06980.2071-0.13790.18180.0433-0.09780.05430.15720.0006-0.00280.1644-0.01590.221550.212620.204346.8253
41.03170.2230.40840.2050.15920.21380.0893-0.05820.10170.1203-0.1503-0.00260.0902-0.05570.0610.1907-0.0608-0.00120.2086-0.01150.195559.992235.42364.0442
51.7299-0.0204-0.99980.4850.35461.14030.1114-0.05620.01920.1661-0.07850.07850.13210.0061-0.03290.2218-0.0202-0.00320.11980.03930.177158.146720.898665.7366
60.9589-0.798-0.07931.7402-0.45330.2699-0.12940.0194-0.00250.02530.0414-0.16050.0446-0.080.0880.1404-0.08150.05750.2672-0.08410.101151.350843.151881.2227
70.57540.8014-0.53871.99280.21632.0831-0.14860.13850.1256-0.09210.30130.01110.1104-0.1293-0.15270.0727-0.0011-0.06790.3075-0.09050.2146.993749.770974.5072
81.64921.09263.74821.97993.21288.9485-0.0461-0.34160.1433-0.0579-0.28940.1866-0.0814-0.75510.33540.0201-0.03450.0460.391-0.16660.163634.209644.613365.5327
91.0107-0.23660.25472.7782-2.85483.14650.049-0.33210.1510.3143-0.1848-0.0449-0.4186-0.07450.13580.21170.06350.00740.3734-0.15390.169935.311344.851443.1955
100.6976-0.2458-0.24170.12920.26381.0567-0.0539-0.03250.18430.0103-0.0539-0.05590.041-0.11290.10780.1507-0.00310.00290.2-0.03040.212942.770738.928750.0856
110.9906-1.26220.74254.2427-2.95342.090.01610.05520.33810.2915-0.0297-0.1139-0.2421-0.01340.01350.20810.0226-0.03490.1147-0.00290.260944.573153.47150.2364
121.14810.42791.1370.9381.60652.9231-0.04440.2780.1567-0.13050.0023-0.0112-0.21080.13430.04210.17090.05850.00820.1589-0.03020.20535.756242.466130.1791
131.1204-1.1457-0.97675.50623.74035.2106-0.04990.09230.1595-0.3019-0.00760.5224-0.2141-0.18060.05750.0590.0456-0.04960.2277-0.02920.237625.607141.302825.5931
140.6508-0.0915-0.03321.91060.80510.33960.02580.0315-0.08950.27050.1623-0.44710.11250.073-0.1880.11230.00190.03050.197-0.09060.262854.8384-0.04935.7731
150.82240.44840.91581.46680.52051.02830.0346-0.0332-0.06460.07240.0323-0.12590.0626-0.0052-0.06680.1383-0.02240.07810.2174-0.04760.180347.569315.105417.9401
160.71220.37890.25840.3390.08310.61870.0095-0.1390.0363-0.0957-0.09580.0158-0.0886-0.02350.08630.1495-0.00330.0490.2185-0.04170.195640.656920.795311.891
170.56630.33540.48790.31760.45030.808-0.0831-0.0131-0.0563-0.15460.06810.0067-0.08150.07660.0150.2333-0.0197-0.00230.1858-0.03410.146630.82455.1902-4.9063
181.8746-0.11511.161.14410.61461.3079-0.15540.11810.29-0.20310.0699-0.1485-0.0420.08850.08550.2776-0.08580.05060.14060.00540.117636.699818.2228-8.1577
190.83610.7162-0.241.3957-1.02780.9421-0.2630.13570.0015-0.09230.1965-0.0836-0.0332-0.09530.06650.22860.0452-0.06850.1996-0.05890.135912.56615.916-14.2751
200.06040.0194-0.17720.0312-0.13090.772-0.08870.0151-0.00970.0302-0.0203-0.00560.0459-0.06940.10910.2090.0147-0.00350.2665-0.09180.25759.37511.7945-5.3146
211.02191.19451.34591.56662.12673.57160.0489-0.166-0.0314-0.0147-0.20760.027-0.1372-0.28680.15860.12060.1217-0.05580.2097-0.12480.22247.637212.1787.206
223.13-0.69471.90255.5394-1.38141.3727-0.0349-0.2625-0.1249-0.04150.0210.2279-0.0314-0.1940.01390.1338-0.02430.06710.231-0.06670.221918.46268.666125.9837
230.5429-0.35460.50761.0771-0.35591.4132-0.0649-0.1257-0.0461-0.1039-0.09080.03160.0172-0.15470.15570.1493-0.00570.02030.18-0.02040.183823.8210.090215.6415
240.98910.5432-1.5352.2772-0.87652.3844-0.04350.1461-0.09960.0318-0.10510.0240.0825-0.22470.14860.1463-0.07560.0510.1813-0.03640.189916.5891-2.5117.3268
252.0622-0.01420.17570.61360.56430.5416-0.0598-0.36790.01250.1663-0.07590.12580.1509-0.07650.13570.16-0.0910.06260.32150.0270.133826.07998.14836.9291
262.1284-0.49761.67590.33160.0153.35970.0731-0.3668-0.10370.091-0.07820.1630.2244-0.26730.00510.1161-0.06550.08160.2937-0.09140.156421.828714.115845.055
271.66040.2325-0.95520.1799-0.28410.70790.020.16110.0128-0.00610.14150.17380.0138-0.22-0.16140.1825-0.01420.04870.13180.09880.258663.347439.5569103.4783
280.54770.01870.04650.0213-0.00580.01590.00060.0390.0725-0.05210.00060.04690.0339-0.0313-0.00120.2880.012-0.00310.1660.01820.180177.986347.845691.3759
290.64450.2691-0.37531.515-1.21321.03990.0282-0.04120.06110.0779-0.0914-0.1371-0.03380.02040.06320.2136-0.01490.01990.15280.03580.156886.848448.535997.4142
300.1765-0.33270.40331.1863-0.60180.9890.0552-0.02330.00170.1245-0.07440.07710.1542-0.05740.01910.2008-0.03790.03160.1640.05340.199485.88930.0255114.1984
312.28920.04470.31480.9954-0.83820.90790.0805-0.07470.01150.2553-0.0729-0.0559-0.15370.04-0.00770.2451-0.05620.02260.1147-0.00260.151388.767144.1034117.4125
320.0231-0.1954-0.14611.88631.43611.1026-0.02210.0054-0.00170.0146-0.05850.057-0.0135-0.01890.08060.1167-0.0284-0.06960.21160.1220.2059100.810219.995123.5728
330.59680.21770.44211.3795-0.46740.7539-0.15160.13380.0260.05190.0085-0.2284-0.00520.06470.14310.2052-0.020.04820.25120.08550.2176101.043514.8607114.5772
340.2289-0.23690.10030.2931-0.0530.11320.07950.10360.0316-0.0509-0.12540.00350.1180.07150.04580.15770.07150.00870.25860.17650.2208108.832321.9968101.773
351.54771.87971.52792.73181.05072.97850.1792-0.0526-0.02850.1778-0.2572-0.05880.27620.26510.07790.2790.0480.01130.18950.02410.240297.855325.606783.1598
362.26891.89190.87681.77060.54222.06050.1118-0.01310.01530.1875-0.20310.06590.02140.15730.09130.21-0.02970.02290.1890.02120.209394.537129.851393.5727
371.77141.5331-0.53352.68712.27175.70670.0904-0.1441-0.29810.2923-0.1284-0.28790.53250.05370.03790.30010.05720.00020.04320.05310.19792.880915.453191.8676
381.0607-0.4364-0.29352.4323-1.36191.06060.04660.1177-0.0688-0.362-0.1523-0.06810.20870.0290.10570.29550.0581-0.01010.17540.03790.131391.708830.19672.1776
390.8746-0.19511.17940.229-0.49181.89140.0380.2469-0.091-0.2328-0.0551-0.0990.29810.28560.01710.32630.0720.12490.20830.02720.160197.985832.208364.1385
400.1727-0.2621-0.0761.475-0.59970.70780.027-0.0721-0.01620.30260.12230.2052-0.2463-0.1043-0.14940.12570.04650.05780.22520.02490.253163.326674.533566.7572
410.3276-0.1065-0.34940.0760.04640.5446-0.0116-0.0919-0.00450.0610.05540.0648-0.1043-0.0244-0.04380.13010.00810.00920.2250.05860.232475.31258.242871.9693
420.65520.23450.24412.2877-1.33451.4355-0.0195-0.0668-0.0531-0.27370.0313-0.06180.1431-0.0013-0.01180.10570.02380.03640.17640.03850.216778.411753.670762.5753
430.0644-0.22160.15770.8746-0.61370.4527-0.0062-0.0090.0382-0.12430.0184-0.04630.04580.0049-0.01220.19960.03030.01290.17270.01050.203579.470371.928645.4415
440.5489-0.5631-0.59721.3701-0.19821.9221-0.07190.02910.0502-0.18480.163-0.03420.2242-0.0826-0.09110.1822-0.0584-0.04860.15590.0150.162972.540258.880443.6705
450.95010.55341.30080.34270.79911.88160.01950.0220.04770.0667-0.0282-0.0020.1518-0.06040.00870.2940.03480.07430.20530.05270.159691.023972.996428.3563
460.39550.1110.70121.4059-0.46121.5958-0.02410.06020.08970.0699-0.2672-0.19480.04620.29210.29130.19930.12510.09010.18030.08350.20198.468475.986334.9278
470.4601-0.68411.33534.8983-4.63225.69890.10790.08950.091-0.1095-0.3004-0.11680.26680.31930.19250.09960.1280.0910.23390.05630.2041105.470364.358843.7905
480.1304-0.04430.29661.23852.13864.8983-0.02540.01260.0462-0.16190.1294-0.0957-0.14850.3691-0.1040.1648-0.03960.00660.17180.03310.2194104.743665.203166.1692
490.3156-0.0861-0.58350.02570.15111.16230.0606-0.05340.0703-0.03420.0029-0.0122-0.00710.1498-0.06350.19640.04190.02470.17950.01410.213395.163664.758259.4908
502.74161.49091.41963.6392.051.31920.06440.06060.0643-0.22810.0199-0.2437-0.12160.0436-0.08430.2082-0.09080.03340.15270.04260.1887102.383277.40559.1791
511.3534-0.00890.30961.5402-2.33433.6062-0.1465-0.19550.17160.18560.0284-0.0591-0.3078-0.06570.11820.10910.03610.02340.22960.00050.1888103.342263.421679.3008
521.5029-0.5818-0.14960.82111.06991.73820.02260.0355-0.06490.06070.2538-0.16610.0780.3812-0.27630.08220.0294-0.05390.29430.02370.1794110.844356.680583.4243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 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
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