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- PDB-2q0z: Crystal structure of Q9P172/Sec63 from Homo sapiens. Northeast St... -

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Basic information

Entry
Database: PDB / ID: 2q0z
TitleCrystal structure of Q9P172/Sec63 from Homo sapiens. Northeast Structural Genomics Target HR1979.
ComponentsProtein PRO2281
KeywordsPROTEIN TRANSPORT / sec63 / sec / NESG / hr1979 / structural genomics / translocase / Northeast Structural Genomics Consortium / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / C2 domain ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / C2 domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
U5 small nuclear ribonucleoprotein 200 kDa helicase / PRO2281
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBenach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. ...Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q9P172/Sec63 from Homo sapiens.
Authors: Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / ...Authors: Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Protein PRO2281


Theoretical massNumber of molelcules
Total (without water)39,0921
Polymers39,0921
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.550, 94.550, 74.109
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein PRO2281


Mass: 39092.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Plasmid: pET14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9P172, UniProt: O75643*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M K/Na tartrate, 0.1M Sodium citrate pH 5.6, 1M Ammonium sulfate, 0.5M Imidazole pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 11.3 % / Av σ(I) over netI: 8.2 / Number: 662162 / Rmerge(I) obs: 0.102 / Χ2: 0.69 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 58497 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.210.0431.01311.6
3.254.0910010.0561.11111.6
2.843.2510010.0640.71811.8
2.582.8410010.0930.5711.7
2.392.5810010.1180.47811.7
2.252.3910010.1780.59711.5
2.142.2510010.2370.77511.3
2.052.1410010.2710.62311.1
1.972.0510010.2720.37310.7
1.91.9710010.4850.60610.2
ReflectionResolution: 1.9→50 Å / Num. obs: 58497 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.102 / Χ2: 0.69 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9710.20.48558320.606100
1.97-2.0510.70.27258560.373100
2.05-2.1411.10.27158920.623100
2.14-2.2511.30.23758340.775100
2.25-2.3911.50.17858360.597100
2.39-2.5811.70.11858410.478100
2.58-2.8411.70.09358730.57100
2.84-3.2511.80.06458630.718100
3.25-4.0911.60.05658541.111100
4.09-5011.60.04358161.01399.2

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.71 / FOM acentric: 0.72 / FOM centric: 0.65 / Reflection: 28346 / Reflection acentric: 25916 / Reflection centric: 2430
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.4-47.2750.880.90.7913741062312
3.4-5.40.910.920.8340203545475
2.7-3.40.820.830.6850864633453
2.4-2.70.730.740.5949894608381
2-2.40.650.660.5781477610537
1.9-20.470.480.3947304458272

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.22 4440 8.9 %
Rwork0.196 --
obs-45263 90.5 %
Solvent computationBsol: 50.839 Å2
Displacement parametersBiso mean: 19.823 Å2
Baniso -1Baniso -2Baniso -3
1--0.432 Å2-0.961 Å20 Å2
2---0.432 Å20 Å2
3---0.865 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 0 265 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0631.5
X-RAY DIFFRACTIONc_scbond_it3.6322
X-RAY DIFFRACTIONc_mcangle_it3.3222
X-RAY DIFFRACTIONc_scangle_it5.7962.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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