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- PDB-6sho: SAD structure of Human Survivin recovered by continuous rotation ... -

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Basic information

Entry
Database: PDB / ID: 6sho
TitleSAD structure of Human Survivin recovered by continuous rotation data collection and multivariate analysis of Friedel pairs
ComponentsBaculoviral IAP repeat-containing protein 5
KeywordsAPOPTOSIS / Multivariate analysis / Single-wavelength X-ray Anomalous Diffraction / Continuous rotation / Human survivin
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cobalt ion binding / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / positive regulation of mitotic cell cycle / RHO GTPases Activate Formins / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle microtubule / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Neddylation / mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.20008450383 Å
AuthorsGarcia-Bonete, M.J. / Katona, G.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Acta Crystallogr.,Sect.A / Year: 2019
Title: Bayesian machine learning improves single-wavelength anomalous diffraction phasing.
Authors: Garcia-Bonete, M.J. / Katona, G.
History
DepositionAug 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: Baculoviral IAP repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9604
Polymers32,8292
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-12 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.980, 71.020, 81.340
Angle α, β, γ (deg.)90.000, 128.475, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 6 - 139 / Label seq-ID: 6 - 139

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16414.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pHis8
Details (production host): Kanamycin resistance, IPTG inducible
Production host: Escherichia coli BL21(DE3) (bacteria)
Variant (production host): One Shot Chemically Competent E. coli
References: UniProt: O15392
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 4.03 Å3/Da / Density % sol: 69.5 % / Description: rod-like crystals, size less 100 um
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaCitrate pH 6.5, 0.1 M BisTris Propane and 20% PEG3500
Temp details: temperature control room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.27265 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27265 Å / Relative weight: 1
ReflectionResolution: 3.2→35.6 Å / Num. obs: 16783 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 96.21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.04
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 1248 / CC1/2: 0.787 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.20008450383→35.590957886 Å / SU ML: 0.446421349697 / Cross valid method: FREE R-VALUE / σ(F): 0.0756043713934 / Phase error: 33.5614454948
RfactorNum. reflection% reflection
Rfree0.259200622153 794 4.86281234689 %
Rwork0.200773223157 --
obs0.203720243151 16328 99.161909389 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 106.670949956 Å2
Refinement stepCycle: LAST / Resolution: 3.20008450383→35.590957886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 2 0 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01146344263382264
X-RAY DIFFRACTIONf_angle_d1.182897533443044
X-RAY DIFFRACTIONf_chiral_restr0.0643341828899308
X-RAY DIFFRACTIONf_plane_restr0.00973092816366402
X-RAY DIFFRACTIONf_dihedral_angle_d7.266302908721390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40040.3949748648041340.3215866760842552X-RAY DIFFRACTION98.8954344624
3.4004-3.66270.3157491574621140.2647950002372638X-RAY DIFFRACTION99.2426974396
3.6627-4.03090.3009741260511380.2205567082372576X-RAY DIFFRACTION99.3775173929
4.0309-4.61310.2313301243171220.1803980285972587X-RAY DIFFRACTION99.449339207
4.6131-5.80790.2134969042461290.1803253260832608X-RAY DIFFRACTION99.1307497284
5.8079-35.590.25059835821570.1782468538882573X-RAY DIFFRACTION98.8772183991
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)
11.67904823952-1.0886954943-3.46921400988-0.3113684661030.4765340792934.170392807420.330777349975-0.1506080586840.4473592809950.1436946485070.841281334953-0.3571079601151.043557255060.472870087022-1.21069937161.29321414029-0.03029039063240.1915162238030.8043765117810.03371619940151.0742958771729.205378241124.9760950139-3.23341966456
28.070360072932.013041320553.845385691659.620103109663.41346435678.50427583404-0.0656014818206-0.2802826513681.664492752640.358115507703-0.1384392036520.957202625438-0.920504514735-0.2233474792180.01146882500670.7311056163970.07165006974990.1570068334880.638164384964-0.1934804362271.1902315013912.015766136544.365120792330.0660605017
39.111266132520.5018256154320.398036402141-0.7713149345170.5282979471160.316435528552-0.685644990175-0.6905498418510.1535395209240.5021418333610.264441873373-0.0796842900110.0275416773605-0.09975046352280.3779830006861.18787734377-0.03164754594310.3308713681150.694376692321-0.1036215267941.45349361754-5.5939032638430.259477266432.7028029297
46.50292731751-1.68345080457-0.2315740498693.34148459345.073761618968.56854997754-0.587385818682-1.064191149420.008017465707650.8210536095950.03117751280450.9620075833730.643211371325-0.1217806299510.4942212853920.7747426737870.007781896388970.0806162915520.726073420412-0.1862385787670.69268886987423.485736049710.363484388211.494781582
58.797208445110.975943544722-1.618280823386.57827994676-1.083395011924.715994268020.239480785420.800320049259-0.549809191242-1.17654830991-0.0217893745441-0.8845755298420.7394201823850.48794652623-0.2955226613840.9957846660950.1042826490970.1545555453550.73945445665-0.172142674280.65965946283531.415701882511.97726884144.52810253826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 140 )
2X-RAY DIFFRACTION2chain 'B' and (resid 6 through 97 )
3X-RAY DIFFRACTION3chain 'B' and (resid 98 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 6 through 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 90 )

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