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- PDB-3mfn: Dfer_2879 protein of unknown function from Dyadobacter fermentans -

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Basic information

Entry
Database: PDB / ID: 3mfn
TitleDfer_2879 protein of unknown function from Dyadobacter fermentans
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDomain of unknown function DUF5618 / Domain of unknown function (DUF5618) / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / ACETATE ION / DUF5618 domain-containing protein
Function and homology information
Biological speciesDyadobacter fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsOsipiuk, J. / Xu, X. / Cui, H. / Chin, S. / Eisen, J. / Wu, D. / Kerfeld, C. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of Dfer_2879 protein of unknown function from Dyadobacter fermentans.
Authors: Osipiuk, J. / Xu, X. / Cui, H. / Chin, S. / Eisen, J. / Wu, D. / Kerfeld, C. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7155
Polymers72,6564
Non-polymers591
Water2,612145
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3873
Polymers36,3282
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-4 kcal/mol
Surface area12730 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)36,3282
Polymers36,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-4 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.779, 83.650, 93.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uncharacterized protein


Mass: 18163.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dyadobacter fermentans (bacteria) / Strain: DSM 18053 / Gene: Dfer_2879 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6W4J3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M sodium acetate, 0.2 M ammonium acetate, 30% PEG-4000, 1/70 chymotrypsin, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→35.3 Å / Num. all: 36244 / Num. obs: 36244 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.092 / Χ2: 2.098 / Net I/σ(I): 9
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.67 / Num. unique all: 1770 / Χ2: 1.025 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→35.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 10.241 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.196 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1802 5 %RANDOM
Rwork0.188 ---
all0.19 36178 --
obs0.19 36178 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.62 Å2 / Biso mean: 24.985 Å2 / Biso min: 9.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---2.11 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.02→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 4 145 4158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224309
X-RAY DIFFRACTIONr_bond_other_d0.0010.022992
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9415826
X-RAY DIFFRACTIONr_angle_other_deg0.92737292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53824.342228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31415816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4781526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
X-RAY DIFFRACTIONr_mcbond_it0.8381.52532
X-RAY DIFFRACTIONr_mcbond_other0.2411.51058
X-RAY DIFFRACTIONr_mcangle_it1.48324054
X-RAY DIFFRACTIONr_scbond_it2.41131777
X-RAY DIFFRACTIONr_scangle_it3.7274.51743
LS refinement shellResolution: 2.024→2.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 109 -
Rwork0.269 2249 -
all-2358 -
obs-2358 89.86 %
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)
13.44310.2745-1.4331.3980.22312.33410.1265-0.35160.20650.04640.0269-0.09240.18370.2276-0.15340.09220.0125-0.0120.1291-0.02480.0578-4.723295.1301-2.5433
23.5774-0.1098-0.61164.1065-0.43381.9195-0.27430.5787-0.0263-0.52190.17320.09150.1652-0.35630.10110.2025-0.0666-0.01270.244-0.02840.0107-14.022786.8505-20.3211
32.4055-0.8446-1.03432.228-0.50992.38510.41640.21930.9866-0.4534-0.1283-0.2687-0.2538-0.2284-0.28810.25420.04830.18370.13830.09040.522-16.5655117.3138-9.6098
43.42070.3312-0.83124.7853-1.15892.6348-0.4686-0.2094-0.8259-0.1250.15290.04410.7676-0.15020.31570.4707-0.03010.22760.1624-0.02460.3975-14.960764.1848-7.3262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 133
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A136 - 184
4X-RAY DIFFRACTION2B7 - 132
5X-RAY DIFFRACTION2B136 - 177
6X-RAY DIFFRACTION3C7 - 131
7X-RAY DIFFRACTION3C136 - 176
8X-RAY DIFFRACTION4D7 - 132
9X-RAY DIFFRACTION4D136 - 148

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