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- PDB-7c4h: Crystal structure of BCP1 from Saccharomyces Cerevisiae -

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Basic information

Entry
Database: PDB / ID: 7c4h
TitleCrystal structure of BCP1 from Saccharomyces Cerevisiae
ComponentsProtein BCP1
KeywordsCHAPERONE / ribosome biosynthesis
Function / homologyBCP1 family / BCCIP / ribosomal large subunit export from nucleus / protein folding chaperone / protein export from nucleus / nucleus / cytoplasm / Protein BCP1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsChang, W.C. / Lin, M.H. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-002-011- Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013- Taiwan
CitationJournal: J.Struct.Biol. / Year: 2020
Title: The crystal structure of protein-transporting chaperone BCP1 from Saccharomyces cerevisiae.
Authors: Lin, M.H. / Kuo, P.C. / Chiu, Y.C. / Chang, Y.Y. / Chen, S.C. / Hsu, C.H.
History
DepositionMay 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BCP1
B: Protein BCP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5913
Polymers67,5512
Non-polymers401
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-28 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.794, 127.794, 127.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein BCP1


Mass: 33775.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BCP1, YDR361C / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06338
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 100 mM sodium citrate tribasic dihydrate (pH 5.2), 32% v/v polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 61457 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 14.31 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.17
Reflection shellResolution: 1.83→1.9 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 6.03 / Num. unique obs: 6068

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→26.09 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 2011 3.27 %
Rwork0.1672 59408 -
obs0.168 61419 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.16 Å2 / Biso mean: 18.777 Å2 / Biso min: 5.38 Å2
Refinement stepCycle: final / Resolution: 1.83→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 1 300 4045
Biso mean--22.84 23.43 -
Num. residues----456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.83-1.870.22821390.18741914330
1.87-1.930.20761450.196142174362
1.93-1.980.19511420.178741784320
1.98-2.050.19621410.162142264367
2.05-2.120.21081440.165342214365
2.12-2.20.19081440.162442444388
2.2-2.30.19931420.178441904332
2.3-2.430.19561450.166142254370
2.43-2.580.22611450.172542264371
2.58-2.780.19041440.175142594403
2.78-3.050.21051430.184642244367
3.06-3.50.19961440.180942824426
3.5-4.40.18851480.148943134461
4.4-26.090.1561450.142644124557
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)
1-0.15950.0311-0.0376-0.0571-0.02030.0211-0.04690.0397-0.0432-0.0276-0.0508-0.01050.0331-0.0005-0.02330.15980.0121-0.00360.0966-0.01380.084833.4919-30.21911.0353
20.23240.0269-0.13250.2673-0.18090.1850.06420.0239-0.0542-0.0391-0.0568-0.03270.00290.0781-0.02240.07950.00880.00780.0604-0.00380.031940.678-23.654321.1948
30.0367-0.04280.02040.0067-0.03630.03720.0024-0.00590.0308-0.0107-0.00980.0068-0.1233-0.0566-0.00480.11390.01010.00260.0748-0.0080.046736.3407-17.253633.2088
40.0211-0.03890.0040.1043-0.06490.1284-0.157-0.06780.04750.3646-0.00860.0843-0.1474-0.1268-0.02290.21310.04760.03220.138-0.03180.118531.2202-8.209339.7948
50.2144-0.24310.15720.38640.00790.0814-0.00990.02740.1042-0.0784-0.0410.0675-0.09670.0156-0.0550.11520.0019-0.00460.0736-0.00970.075631.1513-13.038420.6602
60.0106-0.02760.04130.0217-0.05050.1698-0.00430.20420.3228-0.0666-0.2443-0.2562-0.27090.0619-0.21260.2364-0.03230.01440.09420.05850.191940.6224-2.413817.5463
70.0702-0.06120.08050.0998-0.08790.0728-0.1306-0.00950.10360.1165-0.0019-0.1843-0.22810.033-0.01430.1237-0.02840.01490.1233-0.02270.186245.5035-3.913127.9119
8-0.0036-0.0234-0.12080.1196-0.06150.2317-0.0423-0.03510.0792-0.0901-0.01590.0435-0.2136-0.0989-0.00910.160.0204-0.00360.0752-0.00320.099528.5342-8.655715.2257
9-0.15330.00660.0045-0.01120.057-0.0013-0.01510.0148-0.07750.0065-0.037-0.04210.0205-0.1029-0.01030.1366-0.0069-0.00990.084-0.00190.082726.8152-30.35961.1864
100.09440.0498-0.10250.19980.26020.19990.00590.0282-0.0220.0098-0.02840.01960.0216-0.0399-0.01560.0889-0.00270.00930.078-0.00710.053422.0339-24.7668-22.1939
110.10230.03840.05170.05210.06990.0438-0.12220.0516-0.0434-0.19850.0766-0.0558-0.1544-0.0209-0.00350.1849-0.00760.00090.10790.00520.071323.3581-13.8472-38.2343
120.09920.1250.06790.34750.02030.1034-0.0070.01070.01860.0568-0.021-0.0323-0.0921-0.0106-0.03120.10060.0040.00260.07120.00540.07329.3772-14.4717-20.8027
130.08170.0582-0.04570.1263-0.11890.2209-0.0031-0.1850.06580.2131-0.25190.1718-0.2320.1152-0.04140.22090.03120.02050.069-0.05120.140418.2673-4.4381-17.7498
140.00080.01420.01390.02610.01410.0222-0.01040.04870.0488-0.2319-0.13070.1574-0.2611-0.1503-0.00150.12790.0385-0.01040.1532-0.03520.161914.2149-7.0263-28.3594
150.0325-0.1006-0.06130.31530.02360.1219-0.01930.04130.03650.0717-0.01740.0046-0.18180.1038-0.00940.1437-0.0092-0.00890.07150.00210.077330.729-9.6636-14.4885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 63 )A37 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 110 )A64 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 134 )A111 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 151 )A135 - 151
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 200 )A152 - 200
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 244 )A201 - 244
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 256 )A245 - 256
8X-RAY DIFFRACTION8chain 'A' and (resid 257 through 291 )A257 - 291
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 63 )B37 - 63
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 124 )B64 - 124
11X-RAY DIFFRACTION11chain 'B' and (resid 125 through 147 )B125 - 147
12X-RAY DIFFRACTION12chain 'B' and (resid 148 through 200 )B148 - 200
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 244 )B201 - 244
14X-RAY DIFFRACTION14chain 'B' and (resid 245 through 256 )B245 - 256
15X-RAY DIFFRACTION15chain 'B' and (resid 257 through 291 )B257 - 291

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