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- PDB-7dkp: Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A r... -

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Basic information

Entry
Database: PDB / ID: 7dkp
TitleCrystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / E. coli Grx2 / GSH
Function / homology
Function and homology information


Glutaredoxin-2 / Glutaredoxin 2, C-terminal / Glutaredoxin 2, C terminal domain / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
CITRATE ANION / GLUTATHIONE / Glutaredoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSreekumar, S.N. / Arockiasamy, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR28766/BRB/10/1701/2018 India
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/2018 India
CitationJournal: To Be Published
Title: Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution
Authors: Sreekumar, S.N. / Arockiasamy, A.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin
B: Glutaredoxin
C: Glutaredoxin
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33011
Polymers97,5334
Non-polymers1,7977
Water23,6721314
1
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8803
Polymers24,3831
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8803
Polymers24,3831
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6912
Polymers24,3831
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8803
Polymers24,3831
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.840, 169.451, 49.842
Angle α, β, γ (deg.)90.000, 93.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutaredoxin / Glutaredoxin 2 (Grx2) / Glutaredoxin glutaredoxin / Glutaredoxin / GrxB family / Glutaredoxin-2 / ...Glutaredoxin 2 (Grx2) / Glutaredoxin glutaredoxin / Glutaredoxin / GrxB family / Glutaredoxin-2 / Glutaredoxin-2 Grx2


Mass: 24383.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TEC2
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: 2D plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v ...Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000. Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size of 150 nl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.449→42.94 Å / Num. obs: 137631 / % possible obs: 94.7 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.055 / Rrim(I) all: 0.113 / Net I/σ(I): 8.7
Reflection shellResolution: 1.449→1.476 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.635 / Num. unique obs: 6882 / CC1/2: 0.759 / Rpim(I) all: 0.349 / Rrim(I) all: 0.726 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSJan 31, 2020 (BUILT 20200131)data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KX4

4kx4


Resolution: 1.45→42.893 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.027 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1604 6877 5 %RANDOM
Rwork0.1383 ---
obs0.1394 131485 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.92 Å2 / Biso mean: 11.935 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.17 Å2
2--0.72 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.45→42.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 119 1314 8246
Biso mean--12.56 25.96 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0137158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176841
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.6619704
X-RAY DIFFRACTIONr_angle_other_deg1.6871.59915903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57922.914350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.312151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0721542
X-RAY DIFFRACTIONr_chiral_restr0.3330.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021392
LS refinement shellResolution: 1.45→1.487 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.22 515 -
Rwork0.198 9397 -
obs--92.21 %

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