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- PDB-6m5d: Human serum albumin (apo form) -

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Basic information

Entry
Database: PDB / ID: 6m5d
TitleHuman serum albumin (apo form)
ComponentsSerum albumin
KeywordsPEPTIDE BINDING PROTEIN / Transporter / Cyclic peptide
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / 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
PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsIto, S. / Senoo, A. / Nagatoishi, S. / Yamamoto, M. / Tsumoto, K. / Wakui, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101001 (Support number 1851) Japan
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
Authors: Ito, S. / Senoo, A. / Nagatoishi, S. / Ohue, M. / Yamamoto, M. / Tsumoto, K. / Wakui, N.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: 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
Revision 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0582
Polymers65,9631
Non-polymers951
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-9 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.697, 182.697, 79.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Serum albumin


Mass: 65962.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 5.05 Å3/Da / Density % sol: 75.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 / Details: PEG400 potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→44.31 Å / Num. obs: 76161 / % possible obs: 91.2 % / Redundancy: 4.203 % / Biso Wilson estimate: 76.308 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.082 / Χ2: 1.118 / Net I/σ(I): 11.76 / Num. measured all: 320073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.56-2.714.0691.2461.075065613472124500.5251.41492.4
2.71-2.94.1970.7591.754953512675118020.730.85893.1
2.9-3.134.2360.3733.454622211787109120.9220.42192.6
3.13-3.434.2570.177.73425251086499890.9810.19191.9
3.43-3.834.2520.08914.6538065981989520.9940.191.2
3.83-4.424.230.05422.9133171867978410.9970.06190.3
4.42-5.44.2370.04528.0427856734165750.9970.05189.6
5.4-7.594.2320.04130.7821277568150280.9980.04688.5
7.59-44.314.1220.02836.9910766321726120.9980.03281.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.34 Å44.31 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.17refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ao6

1ao6


Resolution: 2.6→44.31 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 27.76
RfactorNum. reflection% reflection
Rfree0.2641 3569 4.93 %
Rwork0.2304 --
obs0.2321 72411 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 262.69 Å2 / Biso mean: 113.6096 Å2 / Biso min: 38.8 Å2
Refinement stepCycle: final / Resolution: 2.6→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 5 3 4468
Biso mean--143.13 67.65 -
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.640.37431400.33622808294893
2.64-2.670.3431460.30922821296793
2.67-2.710.35271280.31442837296594
2.71-2.760.42121660.36312790295692
2.76-2.80.44071420.33972812295494
2.8-2.850.33751330.30962853298692
2.85-2.90.30451660.29072748291494
2.9-2.960.3371410.28932790293192
2.96-3.020.29251240.28632842296694
3.02-3.080.32631510.27492747289892
3.08-3.150.2491480.25652818296693
3.15-3.230.26021540.26442756291093
3.23-3.320.28081360.25892788292491
3.32-3.420.31671470.24962774292192
3.42-3.530.30461370.24582778291592
3.53-3.650.31041480.23972732288091
3.65-3.80.18341300.23872741287190
3.8-3.970.26521570.2232751290891
3.97-4.180.28641460.2062713285991
4.18-4.440.21181350.19692717285290
4.45-4.790.28221490.19632698284790
4.79-5.270.17591330.20842720285389
5.27-6.030.24951630.23342662282589
6.03-7.590.26021220.23982674279688
7.59-44.310.22751270.17552472259982
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)
17.60783.8151-4.70158.213-4.31175.37580.5429-0.3911.4730.95330.12580.8391-1.04080.3838-0.27070.6664-0.14310.07760.4236-0.07870.744715.6633-65.644530.4761
24.91972.0849-3.20814.2517-3.07177.8559-1.29791.4401-0.3872-1.59130.8899-0.21881.4007-0.48520.31041.1663-0.58740.14970.9065-0.13270.706224.1711-73.28645.9174
35.19151.7141-2.09632.7825-0.80684.1873-0.32250.9190.6145-0.56590.40610.1389-0.01870.1128-0.0181.0385-0.48230.06030.92030.1180.653634.2188-55.5142.3456
45.00610.07993.00061.4803-0.79277.63890.3336-1.10490.88810.7744-0.4781-0.2495-0.70220.38940.12081.7257-0.78880.16821.3312-0.14510.860847.1584-39.102223.4595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 173 )A4 - 173
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 342 )A174 - 342
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 489 )A343 - 489
4X-RAY DIFFRACTION4chain 'A' and (resid 490 through 582 )A490 - 582

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