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- PDB-4gcm: Crystal structure of a thioredoxine reductase (trxB) from Staphyl... -

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Basic information

Entry
Database: PDB / ID: 4gcm
TitleCrystal structure of a thioredoxine reductase (trxB) from Staphylococcus aureus subsp. aureus Mu50 at 1.80 A resolution
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / FAD/NAD-linked reductases / Pyr redox 2 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a thioredoxine reductase (trxB) from Staphylococcus aureus subsp. aureus Mu50 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Aug 18, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,07811
Polymers68,1782
Non-polymers2,9009
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-38 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.673, 90.655, 145.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase / TRXR


Mass: 34089.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MW2 / Gene: trxB, MW0726 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1
References: UniProt: P66011, thioredoxin-disulfide reductase

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Non-polymers , 6 types, 607 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.00% Glycerol, 1.26M tri-Sodium Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 3, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→29.591 Å / Num. obs: 72528 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.664 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.7721.43224212888198.8
1.86-1.940.5623818314918199.5
1.94-2.030.3483.13629414122199.4
2.03-2.130.2414.33329812960199.5
2.13-2.270.1655.93759214551199.2
2.27-2.440.1287.73473513416198.9
2.44-2.690.09110.23610113933198.3
2.69-3.070.06114.43491313380197.7
3.07-3.870.03722.23530113493195.8
3.87-29.5910.02927.53482313304194.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.591 Å / Cor.coef. Fo:Fc: 0.9607 / Cor.coef. Fo:Fc free: 0.9556 / Occupancy max: 1 / Occupancy min: 0.23 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. HEPES, GLYCEROL, CHLORIDE MODELED ARE PRESENT IN CRYO CONDITIONS. FAD AND NADP ARE LIGANDS OF THE PROTEIN OBTAINED FROM THE EXPRESSION HOST. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS) 6. THE DISULFIDE BOND BETWEEN CYS134 AND CYS137 WAS MODELED AS PARTIALLY CLEAVED, LIKELY INDUCED BY RADIATION DAMAGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 3654 5.04 %RANDOM
Rwork0.1569 ---
obs0.1578 72471 99.36 %-
Displacement parametersBiso max: 121.34 Å2 / Biso mean: 34.6756 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.2402 Å20 Å20 Å2
2--5.093 Å20 Å2
3---3.1473 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 189 598 5477
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2451SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes846HARMONIC5
X-RAY DIFFRACTIONt_it5136HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion699SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6314SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5136HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6990HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion2.62
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2478 247 4.67 %
Rwork0.224 5047 -
all0.2251 5294 -
obs--99.36 %
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)
10.47170.2024-0.26870.5256-0.18810.5746-0.02620.0111-0.02070.0717-0.0006-0.0817-0.06560.05190.02680.0074-0.0045-0.0201-0.0850.0107-0.03215.184846.583235.8893
20.45360.01720.23570.4297-0.30830.4467-0.0093-0.02120.0667-0.0238-0.0001-0.0036-0.04320.00060.00930.0576-0.00730.0107-0.04840.0129-0.010310.463647.947136.4432
30.2770.0646-0.15760.8026-0.13470.8310.0128-0.0321-0.05920.0272-0.0031-0.11990.01320.007-0.0098-0.0315-0.011-0.0357-0.08630.0172-0.02744.310623.563550.8664
40.77060.40740.00660.4723-0.9140.96770.0140.0121-0.07730.01560.04290.01510.03890.0182-0.05680.01540.0012-0.0126-0.03420.00790.01433.037722.489646.3762
50.0381-0.0370.11370.23210.2430.51620.00280.00260.00210.01130.0095-0.01080.01980.0037-0.01230.07670.0107-0.0545-0.04120.032-0.03232.83624.44471.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 310}A3 - 310
2X-RAY DIFFRACTION2{A|401 - 401}A401
3X-RAY DIFFRACTION3{B|2 - 310}B2 - 310
4X-RAY DIFFRACTION4{B|401 - 401}B401
5X-RAY DIFFRACTION5{B|402 - 403}B402 - 403

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