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- PDB-4yod: Crystal structure of a thioredoxin-like protein (BACCAC_02376) fr... -

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Basic information

Entry
Database: PDB / ID: 4yod
TitleCrystal structure of a thioredoxin-like protein (BACCAC_02376) from Bacteroides caccae ATCC 43185 at 1.90 A resolution
Componentsthioredoxin-like protein
KeywordsOXIDOREDUCTASE / Thioredoxin fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF5106 / Domain of unknown function (DUF5106) / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesBacteroides caccae ATCC 43185 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a thioredoxin-like protein (BACCAC_02376) from Bacteroides caccae ATCC 43185 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thioredoxin-like protein


Theoretical massNumber of molelcules
Total (without water)33,4501
Polymers33,4501
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.210, 45.420, 70.670
Angle α, β, γ (deg.)90.000, 97.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein thioredoxin-like protein


Mass: 33449.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae ATCC 43185 (bacteria)
Gene: BACCAC_02376 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZHK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (27-312) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (27-312) 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30% polyethylene glycol 6000, 0.1M Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9184,0.9796,0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015
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
10.91841
20.97961
30.97951
ReflectionResolution: 1.9→28.343 Å / Num. obs: 22102 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 1.77 % / Biso Wilson estimate: 34.007 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.056 / Net I/σ(I): 10.6 / Num. measured all: 72712
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.91-1.980.7830.50526856455640560.702189
1.98-2.060.8250.33637764450842440.46794.1
2.06-2.150.8910.2384.57435431540910.33194.8
2.15-2.260.9340.1775.87230432440620.24593.9
2.26-2.410.9610.1327.47552482544160.18291.5
2.41-2.590.9810.0919.37453428840530.12694.5
2.59-2.850.9910.06212.27532449242180.08693.9
2.85-3.260.9950.04116.46841447239910.05789.2
3.26-4.10.9960.0321.97026447239420.04188.1
4.10.9980.02324.87023455040290.03288.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALENovember 3, 2014 BUILT=20141118data scaling
XDSdata scaling
BUSTER2.10.2refinement
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.343 Å / Cor.coef. Fo:Fc: 0.9583 / Cor.coef. Fo:Fc free: 0.9395 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. CONDITIONS. 3. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1126 5.1 %RANDOM
Rwork0.177 ---
obs0.1789 22078 95.43 %-
Displacement parametersBiso max: 149.89 Å2 / Biso mean: 45.8312 Å2 / Biso min: 21.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.5736 Å20 Å2-2.1054 Å2
2--4.7993 Å20 Å2
3----8.3729 Å2
Refine analyzeLuzzati coordinate error obs: 0.263 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 0 197 2460
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1099SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2335HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2688SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2335HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3178HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion2.85
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.232 126 4.5 %
Rwork0.2203 2676 -
all0.2209 2802 -
obs--95.43 %
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)
10.65440.8034-0.07973.34070.21421.4620.00860.05180.08480.2109-0.01340.0143-0.17870.07880.0048-0.0904-0.02140.0243-0.10820.0038-0.0122.089320.350827.0581
24.192-0.0203-0.34823.4636-0.47432.1959-0.09730.5375-0.196-0.49970.0652-0.29060.22150.08690.0321-0.0856-0.03190.0818-0.0875-0.0496-0.109513.9947-2.92748.0481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|36 - 174}A36 - 174
2X-RAY DIFFRACTION2{A|175 - 312}A175 - 312

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