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- PDB-3s25: Crystal structure of a 7-bladed beta-propeller-like protein (EUBR... -

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Basic information

Entry
Database: PDB / ID: 3s25
TitleCrystal structure of a 7-bladed beta-propeller-like protein (EUBREC_1955) from Eubacterium rectale ATCC 33656 at 1.88 A resolution
ComponentsHypothetical 7-bladed beta-propeller-like protein
KeywordsStructural Genomics / Unknown function / 7-bladed beta-propeller / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF5050 / Domain of unknown function (DUF5050) / membrane => GO:0016020 / DUF5050 domain-containing protein
Function and homology information
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical 7-bladed beta-propeller-like protein (EUBREC_1955, ERE_32420) from Eubacterium rectale at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Dec 24, 2014Group: Structure summary
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical 7-bladed beta-propeller-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,42312
Polymers34,7401
Non-polymers68311
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.649, 118.649, 53.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Hypothetical 7-bladed beta-propeller-like protein


Mass: 34739.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / Gene: ERE_32420, EUBREC_1955 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: C4ZBG5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 30-330) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 30-330) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Description: While data were scaled with XSCALE, the final statistics reported in the REMARK 200 section have been calculated with SCALA with fixed scales and no sd correction
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20.0% polyethylene glycol 6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.96109,0.97929,0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 31, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979291
30.979071
ReflectionResolution: 1.88→41.949 Å / Num. all: 30369 / Num. obs: 30369 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rsym value: 0.028 / Net I/σ(I): 24.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.88-1.984.10.4061.91778743680.40698.6
1.98-2.114.10.2233.51732841950.223100
2.11-2.254.20.1276.11641439500.127100
2.25-2.434.10.0849.31511536720.08499.9
2.43-2.664.10.05514.11387733770.05599.9
2.66-2.984.10.034221258630610.034100
2.98-3.444.10.022301124727150.02299.8
3.44-4.2140.01835.1927122980.01899.4
4.21-5.954.10.01546721217780.01599.5
5.95-41.9493.80.01836.636599550.01895.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
XSCALEDecember 6, 2010data scaling
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.88→41.949 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.307 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 6.THE RAMACHANDRAN OUTLIER AT RESIDUE 323 IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 1545 5.1 %RANDOM
Rwork0.1583 ---
obs0.1595 30369 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 50.2502 Å2 / Biso min: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.88→41.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 44 162 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222584
X-RAY DIFFRACTIONr_bond_other_d0.0010.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9353515
X-RAY DIFFRACTIONr_angle_other_deg0.88634140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2224.795146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8251513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_mcbond_it1.89731530
X-RAY DIFFRACTIONr_mcbond_other0.5113621
X-RAY DIFFRACTIONr_mcangle_it3.06252492
X-RAY DIFFRACTIONr_scbond_it4.44681054
X-RAY DIFFRACTIONr_scangle_it6.272111010
LS refinement shellResolution: 1.883→1.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 106 -
Rwork0.22 2064 -
all-2170 -
obs--97.27 %
Refinement TLS params.Method: refined / Origin x: 11.5981 Å / Origin y: 35.8191 Å / Origin z: 9.6073 Å
111213212223313233
T0.0127 Å2-0.0038 Å20.0081 Å2-0.011 Å2-0.0136 Å2--0.0287 Å2
L1.8224 °2-0.0973 °2-0.2549 °2-1.4632 °2-0.2917 °2--1.5444 °2
S0.0452 Å °-0.0509 Å °0.1021 Å °0.0718 Å °-0.0079 Å °0.0474 Å °0.0078 Å °-0.0746 Å °-0.0373 Å °

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