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- PDB-3bgu: Crystal structure of a dimeric ferredoxin-like protein of unknown... -

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Basic information

Entry
Database: PDB / ID: 3bgu
TitleCrystal structure of a dimeric ferredoxin-like protein of unknown function (tfu_0763) from thermobifida fusca yx at 1.50 A resolution
ComponentsFerredoxin-like protein of unknown function
KeywordsUNKNOWN FUNCTION / Ferredoxin-like fold / stress responsive a/b barrel domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NITROBENZENE / Stress-response A/B barrel domain-containing protein
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dimeric ferredoxin-like protein of unknown function (YP_288824.1) from Thermobifida fusca YX at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-like protein of unknown function
B: Ferredoxin-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,02518
Polymers26,0002
Non-polymers1,02416
Water3,171176
1
A: Ferredoxin-like protein of unknown function
hetero molecules

A: Ferredoxin-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,55926
Polymers26,0002
Non-polymers1,55824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area2400 Å2
MethodPISA
2
B: Ferredoxin-like protein of unknown function
hetero molecules

B: Ferredoxin-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,49110
Polymers26,0002
Non-polymers4908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.070, 35.270, 76.630
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number3
Space group name H-MP121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin-like protein of unknown function


Mass: 13000.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: YP_288824.1, Tfu_0763 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47RW6

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NBZ / NITROBENZENE / Nitrobenzene


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG.

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 50.0% Ethylene glycol, 5.0% PEG 1000, 0.1M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9798, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97981
30.97971
ReflectionResolution: 1.5→27.206 Å / Num. obs: 35092 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.273 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.3971.646054106161.1
1.55-1.620.353285206440179.5
1.62-1.690.2812.8117226502195.6
1.69-1.780.1993.9127916913196.2
1.78-1.890.1355.7126616859196.7
1.89-2.040.0839129847108196.9
2.04-2.240.05113.6121946754196.9
2.24-2.560.03817.3124556952197.4
2.56-3.230.02822123757049197.5
3.23-27.2060.02129.3122406954196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→27.206 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.321 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RAMACHANDRAN OUTLIER OF RESIDUE ASN-5 AND GLU-6 IN SUBUNIT A IS LOCATED IN POOR DENSITY. 5. N-TERMINAL HIS TAG IN CHAIN A (RESIDUES -3 TO -8) IS SEVERELY DISORDERED. 6. ACETATE AND ETHYLENE GLYCOL ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 7. NITROBENZENE (NBZ) WAS MODELED BASED ON ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1762 5 %RANDOM
Rwork0.197 ---
obs0.199 35091 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.6 Å2
2---0.2 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 66 176 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211802
X-RAY DIFFRACTIONr_bond_other_d0.0020.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9532435
X-RAY DIFFRACTIONr_angle_other_deg0.97332869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6115225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90523.97788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39815248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8981511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022071
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
X-RAY DIFFRACTIONr_nbd_refined0.2050.2365
X-RAY DIFFRACTIONr_nbd_other0.1970.21232
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2824
X-RAY DIFFRACTIONr_nbtor_other0.090.2947
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.213
X-RAY DIFFRACTIONr_mcbond_it1.79831132
X-RAY DIFFRACTIONr_mcbond_other0.5293445
X-RAY DIFFRACTIONr_mcangle_it2.5951767
X-RAY DIFFRACTIONr_scbond_it4.4888745
X-RAY DIFFRACTIONr_scangle_it5.56811668
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 103 -
Rwork0.253 1769 -
all-1872 -
obs--67.97 %
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)
10.93310.13470.63650.5355-0.03161.5975-0.0865-0.04150.0707-0.0192-0.00040.0361-0.1012-0.19330.0869-0.08310.0110.0091-0.0346-0.0121-0.001825.7949-26.139135.0825
20.95950.14170.19320.83840.23873.97660.0751-0.08410.01380.0238-0.03790.06850.7631-0.1795-0.03720.1255-0.0493-0.014-0.09610.0009-0.07718.9043-45.39058.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-8 - 9711 - 116
2X-RAY DIFFRACTION2BB-6 - 9713 - 116

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