[English] 日本語
Yorodumi
- PDB-4emx: Crystal structure analysis of Human Serum Albumin in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4emx
TitleCrystal structure analysis of Human Serum Albumin in complex with chloride anions at cryogenic temperature
ComponentsSerum albumin
KeywordsPROTEIN BINDING / plasma / drug binding / antioxidant / allostery / redox biology / all alpha / disulfide bond stabilized / human plasma osmotic regulation / transport / extracellular space / free radicals
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance 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
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBotti, H. / Bonilla, L. / Trajtenberg, F. / Radi, R. / Buschiazzo, A.
CitationJournal: to be published
Title: New insights on B factors in crystal structure analysis and crystallographic model refinement
Authors: Botti, H. / Bonilla, L. / Trajtenberg, F. / Radi, R. / Buschiazzo, A.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3558
Polymers133,1422
Non-polymers2136
Water4,107228
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6784
Polymers66,5711
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6784
Polymers66,5711
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.880, 59.230, 95.610
Angle α, β, γ (deg.)75.170, 87.830, 74.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 199
2114B4 - 199
1123A200 - 389
2123B200 - 389
1131A390 - 582
2131B390 - 582

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 microL 100 mg/mL protein in 50 mM disodium/monosodium phosphate buffer and 100 mM NaCl were mixed with 2 uL 25% PEG 3350, 50 mM disodium/monosodium phosphate buffer, 100 mM NaCl, pH 7.5, ...Details: 2 microL 100 mg/mL protein in 50 mM disodium/monosodium phosphate buffer and 100 mM NaCl were mixed with 2 uL 25% PEG 3350, 50 mM disodium/monosodium phosphate buffer, 100 mM NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2009 / Details: Crystal Type: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.28→25.566 Å / Num. all: 50973 / Num. obs: 50973 / % possible obs: 93.1 % / Redundancy: 2.6 % / Rsym value: 0.066 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.28-2.42.60.3671.91977675790.36795
2.4-2.552.60.2342.91875372100.23495
2.55-2.732.60.1631.21757867320.16394.7
2.73-2.942.60.1076.41644863080.10795
2.94-3.222.60.0788.31495457220.07894.3
3.22-3.612.60.0629.51343551580.06293.9
3.61-4.162.60.0569.31182345120.05692.3
4.16-5.12.60.0511.7929436240.0588.9
5.1-7.212.70.05411.1792028830.05490.6
7.21-25.7232.70.04114.8340112450.04172

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2593 / WRfactor Rwork: 0.2025 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8281 / SU B: 17.279 / SU ML: 0.204 / SU R Cruickshank DPI: 0.4073 / SU Rfree: 0.2479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1010 2 %RANDOM
Rwork0.1873 ---
obs0.1883 49673 93.03 %-
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 max: 185.73 Å2 / Biso mean: 76.1408 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.17 Å2-0.76 Å2
2---0.19 Å21.43 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9079 0 6 228 9313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029362
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9712685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95551176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09624.744430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.462151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9731549
X-RAY DIFFRACTIONr_chiral_restr0.1110.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217040
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11539MEDIUM POSITIONAL0.240.5
11539MEDIUM THERMAL5.312
2693LOOSE POSITIONAL0.075
2745TIGHT THERMAL2.890.5
2693LOOSE THERMAL3.9510
31451TIGHT THERMAL4.610.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 79 -
Rwork0.245 3678 -
all-3757 -
obs--94.73 %
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)
11.47280.08230.33522.3702-0.01773.66960.1635-0.06480.06620.10590.01580.12420.2803-0.6936-0.17930.0983-0.0726-0.01840.1380.03780.0789-8.5357-15.8473-2.8526
21.811.14510.69474.9701-0.58972.2367-0.12260.11570.11510.1335-0.2528-1.3-0.18570.36790.37540.0643-0.0127-0.07750.0810.11630.630819.49090.7674-4.65
34.0880.062-0.64172.72-0.26683.68490.1012-0.42050.3370.85970.1040.2351-0.6212-0.4977-0.20530.53620.07790.11910.16710.07160.2704-9.525915.63357.049
41.18590.5190.9451.35921.20975.00670.1682-0.1513-0.32260.115-0.0519-0.02560.6696-0.6378-0.11630.1081-0.0304-0.02680.39420.06520.1556-22.6481-25.1137-42.9529
52.78380.5453-0.17961.7018-0.73492.55730.00730.10390.26550.0506-0.2614-0.2595-0.42770.3060.25410.11580.03130.00320.31510.17470.16050.7166-2.3891-42.0686
62.15140.97520.07932.97110.82174.61780.02250.3898-0.3459-0.30050.0187-0.39180.68960.1817-0.04120.21390.1082-0.01640.55370.06910.25837.242-34.4656-52.5555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION2A200 - 389
3X-RAY DIFFRACTION3A390 - 582
4X-RAY DIFFRACTION4B2 - 199
5X-RAY DIFFRACTION5B200 - 389
6X-RAY DIFFRACTION6B390 - 582

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more