5GWN

Crystal structure of human RCC2

> Summary

Summary for 5GWN

DescriptorProtein RCC2, SULFATE ION (3 entities in total)
Functional Keywordsseven-bladed propeller, protein binding
Biological sourceHomo sapiens (Human)
Cellular locationNucleus, nucleolus Q9P258
Total number of polymer chains1
Total molecular weight48436.78
Authors
Liang, L.,Yun, C.H.,Yin, Y.X. (deposition date: 2016-09-12, release date: 2017-09-13)
Primary citation
Song, C.,Liang, L.,Jin, Y.,Li, Y.,Liu, Y.,Guo, L.,Wu, C.,Yun, C.H.,Yin, Y.
RCC2 is a novel p53 target in suppressing metastasis
Oncogene, 2017
DOI: 10.1038/onc.2017.306
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.309 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.188101.2%3.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gwn
no rotation
Molmil generated image of 5gwn
rotated about x axis by 90°
Molmil generated image of 5gwn
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AProtein RCC2polymer43947956.51
UniProt (Q9P258)
Pfam (PF00415)
Homo sapiens (Human)Regulator of chromosome condensation 2,RCC1-like protein TD-60,Telophase disk protein of 60 kDa
SULFATE IONnon-polymer96.15
waterwater18.0555

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight47956.5
Non-Polymers*Number of molecules5
Total molecular weight480.3
All*Total molecular weight48436.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.309 Å)

Cell axes94.44784.05660.671
Cell angles90.00101.5790.00
SpacegroupC 1 2 1
Resolution limits40.68 - 1.31
the highest resolution shell value1.324 - 1.309
R-factor0.1721
R-work0.17120
the highest resolution shell value0.263
R-free0.18890
the highest resolution shell value0.302
RMSD bond length0.007
RMSD bond angle1.084

Data Collection Statistics

Resolution limits40.68 - 1.31
the highest resolution shell value -
Number of reflections109282
Completeness98.1
Redundancy12.8
the highest resolution shell value8.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15binding site for residue SO4 A 601
ChainResidue
AARG130
AASN131
ATHR319
ALYS320
ALYS377

AC24binding site for residue SO4 A 602
ChainResidue
AASN135
ATRP137
AHOH704
AHOH709

AC35binding site for residue SO4 A 603
ChainResidue
AASP186
ATHR187
ALYS188
AHOH879
AHOH998

AC45binding site for residue SO4 A 604
ChainResidue
APHE407
ATHR411
AILE442
ATRP453
AHOH899

AC510binding site for residue SO4 A 605
ChainResidue
AVAL308
APRO309
AARG310
AVAL402
AGLY403
AGLY429
ATRP430
AARG431
AHOH729
AHOH737

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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