[English] 日本語
Yorodumi
- PDB-7psp: Crystal structure of S100A4 labeled with NU000846b. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7psp
TitleCrystal structure of S100A4 labeled with NU000846b.
ComponentsProtein S100-A4
KeywordsCYTOSOLIC PROTEIN / Covalent inhibitor / Protein labeling / calcium-binding protein / S100-protein family.
Function / homology
Function and homology information


RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm ...RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Chem-85Q / Protein S100-A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsGiroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. ...Giroud, C. / Szommer, T. / Coxon, C. / Monteiro, O. / Christott, T. / Bennett, J. / Aitmakhanova, K. / Raux, B. / Newman, J. / Elkins, J. / Arruda Bezerra, G. / Krojer, T. / Koekemoer, L. / Von Delft, F. / Bountr, C. / Brennan, P. / Fedorov, O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative115766 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of S100A4 labeled with NU000846b.
Authors: Giroud, C.
History
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein S100-A4
B: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5418
Polymers28,6262
Non-polymers9156
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-53 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.540, 109.540, 89.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

-
Components

#1: Protein Protein S100-A4 / / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4


Mass: 14313.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P26447
#2: Chemical ChemComp-85Q / (2R,4R)-1-(2-chloranylethanoyl)-N-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide


Mass: 377.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Labelled protein in 3M sodium chloride, 0.1M citrate, pH 3.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.61→65.2 Å / Num. obs: 18350 / % possible obs: 99.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 87.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.018 / Rrim(I) all: 0.076 / Net I/av σ(I): 1 / Net I/σ(I): 0.1467
Reflection shellResolution: 2.61→2.68 Å / Num. unique obs: 10160 / CC1/2: 1

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C1V

3c1v


Resolution: 2.61→54.77 Å / SU ML: 0.3732 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.4193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2857 889 4.84 %
Rwork0.2453 17461 -
obs0.2473 18350 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.96 Å2
Refinement stepCycle: LAST / Resolution: 2.61→54.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 67 2 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181586
X-RAY DIFFRACTIONf_angle_d0.51972139
X-RAY DIFFRACTIONf_chiral_restr0.0342229
X-RAY DIFFRACTIONf_plane_restr0.0017281
X-RAY DIFFRACTIONf_dihedral_angle_d20.4269612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.770.42351270.36962926X-RAY DIFFRACTION100
2.77-2.990.34281330.31332918X-RAY DIFFRACTION99.97
2.99-3.290.3971460.36332921X-RAY DIFFRACTION99.97
3.29-3.760.3061580.27182899X-RAY DIFFRACTION100
3.76-4.740.25231550.22772906X-RAY DIFFRACTION99.97
4.74-54.770.26881700.20712891X-RAY DIFFRACTION99.71

+
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