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- PDB-3fdj: The structure of a DegV family protein from Eubacterium eligens. -

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Basic information

Entry
Database: PDB / ID: 3fdj
TitleThe structure of a DegV family protein from Eubacterium eligens.
ComponentsDegV family protein
Keywordsstructural genomics / unknown function / DegV / gut microbiome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rubrerythrin, domain 2 / Single Sheet ...DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DegV family protein
Similarity search - Component
Biological speciesEubacterium eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Hendricks, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a DegV family protein from Eubacterium eligens.
Authors: Cuff, M.E. / Hendricks, R. / Freeman, L. / Joachimiak, A.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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

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Assembly

Deposited unit
A: DegV family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3616
Polymers30,7401
Non-polymers6225
Water5,711317
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.445, 57.445, 186.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DegV family protein


Mass: 30739.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ASSEMBLY.20070618:0-0:0-0 (zvnW5vjFOAACMF8NLOPRFTmWH60:01:1-275) GENE
Source: (gene. exp.) Eubacterium eligens (bacteria)
Gene: ASSEMBLY.20070618:0-0:0-0 (zvnW5vjFOAACMF8NLOPRFTmWH60:01:1-275)
Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VX07*PLUS

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Non-polymers , 6 types, 322 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M sodium acetate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942,0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979291
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 19.87 / Number: 232515 / Rmerge(I) obs: 0.132 / Χ2: 1.46 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 30039 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.885098.310.0813.2896.8
3.884.8899.810.0732.5787
3.393.8899.910.0892.6257.2
3.083.3999.910.1012.1817.4
2.863.0810010.1131.8247.7
2.692.8610010.1241.4937.8
2.552.6910010.1341.3557.9
2.442.5510010.1521.2027.9
2.352.4410010.1631.167.9
2.272.3510010.1730.9968
2.22.2710010.1941.0128
2.132.210010.2150.9668
2.082.1310010.2410.988
2.032.0810010.2760.9488
1.982.0310010.3290.9078
1.941.9810010.3971.2138
1.91.9410010.4881.0487.9
1.861.910010.5781.1348
1.831.8610010.711.3357.9
1.81.8310010.8041.2527.8
ReflectionResolution: 1.8→50 Å / Num. all: 30039 / Num. obs: 30039 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.132 / Χ2: 1.461 / Net I/σ(I): 19.873
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.804 / Num. unique all: 1451 / Χ2: 1.252 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.8 Å / D res low: 50 Å / FOM : 0.289 / FOM acentric: 0.318 / FOM centric: 0.13 / Reflection: 29850 / Reflection acentric: 25156 / Reflection centric: 4694
Phasing MAD set

Highest resolution: 1.8 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.8110.30.200251564694
20.980.9443.959.60.390.31117232841
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
111.5-501.3510.60.4005388
16.5-11.51.7610.70.400362244
14.53-6.51.6810.60.400961372
13.47-4.531.2110.50.4001845525
12.82-3.471.5110.40.3003023663
12.37-2.822.0410.40.2004490807
12.05-2.371.9110.30.1006229929
11.8-2.052.510.20.10081931066
211.5-500.970.943851.10.990.555388
26.5-11.50.920.844454.60.790.61362244
24.53-6.50.960.8949.964.80.560.41961372
23.47-4.530.980.9558.978.20.380.271845524
22.82-3.470.980.9644.857.70.380.273015660
22.37-2.820.980.9737.247.90.330.234422794
22.05-2.370.990.9937.963.70.260.151065159
21.8-2.0500000000
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se18.676670.2470.5540.0480
2Se21.009930.0850.5290.0220
3Se17.957770.2020.3390.0060
4Se52.80426-0.0530.4880.0510
5Se29.45503-0.0040.3440.0710
6Se25.13630.107-0.0540.0620
7Se27.298150.5050.6060.0830
8Se32.102980.0420.4310.1010
9Se29.809220.3290.6350.0050
10Se25.642550.2450.5520.049-0.162
11Se24.522110.0870.5310.021-0.133
12Se25.795820.2020.340.006-0.17
13Se56.59305-0.0510.4890.052-0.156
14Se36.29259-0.0040.3450.072-0.165
15Se24.821840.106-0.0520.062-0.15
16Se24.58460.5050.6070.083-0.187
17Se49.889660.0440.430.101-0.105
18Se59.252870.3340.6350.003-0.19
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.5-500.4210.6450.2861415388
6.5-11.50.5520.6630.387606362244
4.53-6.50.5050.5830.3011333961372
3.47-4.530.4290.4860.22723701845525
2.82-3.470.4060.4520.19836863023663
2.37-2.820.360.40.13652974490807
2.05-2.370.2480.2820.01971586229929
1.8-2.050.1470.1660925981931066
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29850
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.47-10058.60.793501
5.84-7.4746.90.866506
5.01-5.8453.80.889561
4.46-5.0152.20.903608
4.05-4.46560.905677
3.74-4.0555.60.884745
3.49-3.7457.90.877778
3.29-3.4955.80.873827
3.12-3.2955.40.863880
2.97-3.1258.10.875918
2.84-2.9760.60.863950
2.73-2.8458.70.876987
2.63-2.7357.10.8651027
2.54-2.6358.80.8741074
2.46-2.5459.20.8831106
2.38-2.4660.80.8871118
2.31-2.3859.50.8861167
2.25-2.3162.60.8861200
2.19-2.2565.50.8791214
2.14-2.19660.8751238
2.09-2.1466.60.8731310
2.04-2.0970.60.8751291
2-2.0468.40.8681350
1.96-270.20.8621356
1.92-1.9675.30.8471356
1.88-1.9274.10.851410
1.85-1.8873.90.8241409
1.8-1.8576.50.7752286

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.8→48.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.447 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1512 5.1 %RANDOM
Rwork0.16 ---
all0.162 29849 --
obs0.162 29849 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.6 Å2 / Biso mean: 15.938 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 41 317 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222243
X-RAY DIFFRACTIONr_bond_other_d0.0010.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9923016
X-RAY DIFFRACTIONr_angle_other_deg0.873.0033714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85324.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5381513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_mcbond_it0.7341.51416
X-RAY DIFFRACTIONr_mcbond_other0.2141.5589
X-RAY DIFFRACTIONr_mcangle_it1.45222271
X-RAY DIFFRACTIONr_scbond_it2.843827
X-RAY DIFFRACTIONr_scangle_it4.3644.5745
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 123 -
Rwork0.226 1990 -
all-2113 -
obs--97.19 %
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)
11.0077-0.1169-0.04281.5618-0.04940.7317-0.00940.0844-0.0332-0.1608-0.02530.12790.036-0.01810.03470.06370.0104-0.02250.0098-0.00730.015814.2854-2.508235.2832
21.2873-0.2108-0.03581.7889-0.00790.82390.01310.00090.0785-0.021-0.0238-0.0044-0.08670.00270.01070.06850.0031-0.01180.0005-0.00060.007113.902118.277838.2921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 148
2X-RAY DIFFRACTION2A149 - 275

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