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- PDB-4x0x: The structure of AhpE from Mycobacterium tuberculosis revisited -

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Basic information

Entry
Database: PDB / ID: 4x0x
TitleThe structure of AhpE from Mycobacterium tuberculosis revisited
ComponentsPutative peroxiredoxin MT2298
KeywordsOXIDOREDUCTASE / Peroxiredoxins / Protein Structure
Function / homology
Function and homology information


mycoredoxin-dependent peroxiredoxin / peroxidase activity
Similarity search - Function
Peroxiredoxin, AhpC-type / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkyl hydroperoxide reductase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPallo, A. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G030512N Belgium
Citation
Journal: Sci Rep / Year: 2016
Title: Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.
Authors: van Bergen, L.A. / Alonso, M. / Pallo, A. / Nilsson, L. / De Proft, F. / Messens, J.
#1: Journal: J. Mol. Biol. / Year: 2005
Title: Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin.
Authors: Li, S. / Peterson, N.A. / Kim, M.Y. / Kim, C.Y. / Hung, L.W. / Yu, M. / Lekin, T. / Segelke, B.W. / Lott, J.S. / Baker, E.N.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peroxiredoxin MT2298
B: Putative peroxiredoxin MT2298
C: Putative peroxiredoxin MT2298
D: Putative peroxiredoxin MT2298


Theoretical massNumber of molelcules
Total (without water)67,8884
Polymers67,8884
Non-polymers00
Water5,603311
1
A: Putative peroxiredoxin MT2298
B: Putative peroxiredoxin MT2298


Theoretical massNumber of molelcules
Total (without water)33,9442
Polymers33,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: Putative peroxiredoxin MT2298
D: Putative peroxiredoxin MT2298


Theoretical massNumber of molelcules
Total (without water)33,9442
Polymers33,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-13 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.199, 148.199, 33.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA0 - 1511 - 152
21LEULEUBB0 - 1511 - 152
12LEULEUAA0 - 1511 - 152
22LEULEUCC0 - 1511 - 152
13LEULEUAA0 - 1511 - 152
23LEULEUDD0 - 1511 - 152
14ALAALABB0 - 1531 - 154
24ALAALACC0 - 1531 - 154
15ALAALABB0 - 1531 - 154
25ALAALADD0 - 1531 - 154
16ALAALACC0 - 1531 - 154
26ALAALADD0 - 1531 - 154

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative peroxiredoxin MT2298 / Thioredoxin reductase


Mass: 16972.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: MT2298 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIE2, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.8M sodium malonate pH 5.0 mixed with 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.91983 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 56084 / % possible obs: 99.83 % / Rsym value: 0.082 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.29 / Num. unique all: 5817 / Rsym value: 0.598 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
REFMAC3.15refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xvw

1xvw


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.2073 / FOM work R set: 0.8068 / SU B: 7.824 / SU ML: 0.115 / SU R Cruickshank DPI: 0.16 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2986 5.1 %RANDOM
Rwork0.2186 56084 --
obs0.2202 56084 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.94 Å2 / Biso mean: 23.74 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-0 Å2
2--0.95 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: final / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 0 311 5082
Biso mean---31.39 -
Num. residues----615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194920
X-RAY DIFFRACTIONr_bond_other_d0.0110.024608
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9386707
X-RAY DIFFRACTIONr_angle_other_deg1.664310536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36423.734241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31915736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8421537
X-RAY DIFFRACTIONr_chiral_restr0.1090.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.0215733
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021230
X-RAY DIFFRACTIONr_mcbond_it2.1221.7442466
X-RAY DIFFRACTIONr_mcbond_other2.1161.7432465
X-RAY DIFFRACTIONr_mcangle_it3.1313.2463078
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87500.11
12B87500.11
21A87720.11
22C87720.11
31A87760.09
32D87760.09
41B92100.07
42C92100.07
51B86790.12
52D86790.12
61C87150.12
62D87150.12
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 235 -
Rwork0.252 4073 -
all-4308 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: -36.17 Å / Origin y: 38.1751 Å / Origin z: 11.6834 Å
111213212223313233
T0.0022 Å20.0005 Å2-0.0042 Å2-0.0028 Å20.0024 Å2--0.0621 Å2
L0.1254 °20.012 °2-0.0001 °2-0.1558 °20.0074 °2--0.2368 °2
S0.0124 Å °0.0139 Å °0.0098 Å °0.0101 Å °-0.0113 Å °0.0061 Å °0.0013 Å °-0.0068 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION1B1 - 153
3X-RAY DIFFRACTION1C1 - 153
4X-RAY DIFFRACTION1D1 - 153

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