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- PDB-4ftd: Crystal structure of a DUF4623 family protein (BACEGG_03550) from... -

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Basic information

Entry
Database: PDB / ID: 4ftd
TitleCrystal structure of a DUF4623 family protein (BACEGG_03550) from Bacteroides eggerthii DSM 20697 at 1.91 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 6-bladed-beta-propeller / immunoglobulin-like / carbohydrate metabolism / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #2340 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein (BACEGG_03550) from Bacteroides eggerthii DSM 20697 at 1.91 A resolution (CASP Target)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4963
Polymers50,3121
Non-polymers1842
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.428, 60.391, 81.109
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein


Mass: 50311.938 Da / Num. of mol.: 1 / Fragment: UNP residues 23-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_03550 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AM82
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THIS CONSTRUCT (RESIDUES 23-474) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THIS CONSTRUCT (RESIDUES 23-474) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE ELECTRON DENSITY FOR RESIDUE 154 LOOKS MORE LIKE A LEUCINE THAN PHENYLALANINE. HOWEVER, DNA SEQUENCING OF THE CLONED CONSTRUCT CONFIRMS THE ASSIGNMENT OF PHENYLALANINE AT POSITION 154.

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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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.00% 2-propanol, 20.00% polyethylene glycol 4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795,0.9793,0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled 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
10.97951
20.97931
30.91841
ReflectionResolution: 1.91→45.537 Å / Num. obs: 51287 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.067 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.68
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.0122.1412695194197.2
1.98-2.060.0123402515132197.8
2.06-2.150.0124.1367924883197.5
2.15-2.260.0125.3374094907196.3
2.26-2.410.0126.8437875477198.5
2.41-2.590.0129.4394204976198.3
2.59-2.850.01213.4378135076196.4
2.85-3.260.01220.6413045196198.9
3.26-4.10.01228.1379425161197.7
4.1-45.5370.01232.8391185350197.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→45.537 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.641 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101
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.GLYCEROL (GOL) USED AS CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2613 5.1 %RANDOM
Rwork0.1535 ---
obs0.1551 51279 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 189.11 Å2 / Biso mean: 55.3896 Å2 / Biso min: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20.73 Å2
2--2.12 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 1.91→45.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 12 365 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023488
X-RAY DIFFRACTIONr_bond_other_d0.0020.022330
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9624727
X-RAY DIFFRACTIONr_angle_other_deg1.09935714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6365445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07825.127158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97415588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 181 -
Rwork0.278 3478 -
all-3659 -
obs--97.39 %
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)
15.12682.9279-1.57943.9962-0.94654.08870.0729-0.56520.24390.1995-0.212-0.0084-0.05990.40470.13910.11920.0015-0.040.2491-0.02830.119957.49168.9446-27.0861
21.64710.1648-0.30071.4304-0.16532.5499-0.0620.2078-0.0252-0.25710.0434-0.01090.12340.2280.01860.07220.0023-0.01440.0573-0.01290.084546.20051.308824.1069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 133
2X-RAY DIFFRACTION2A134 - 474

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