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- PDB-4evm: 1.5 Angstrom crystal structure of soluble domain of membrane-anch... -

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Basic information

Entry
Database: PDB / ID: 4evm
Title1.5 Angstrom crystal structure of soluble domain of membrane-anchored thioredoxin family protein from Streptococcus pneumoniae strain Canada MDR_19A
ComponentsThioredoxin family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha/beta protein / thioredoxin fold / thioredoxin-like superfamily / TlpA-like family / Glutathione peroxidase-like family
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin family protein / Thioredoxin family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.506 Å
AuthorsWawrzak, Z. / Stogios, P.J. / Minasov, G. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.5 Angstrom crystal structure of soluble domain of membrane-anchored thioredoxin family protein from Streptococcus pneumoniae strain Canada MDR_19A
Authors: Wawrzak, Z. / Stogios, P.J. / Minasov, G. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin family protein


Theoretical massNumber of molelcules
Total (without water)15,5241
Polymers15,5241
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.247, 63.247, 89.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin family protein


Mass: 15523.678 Da / Num. of mol.: 1 / Fragment: UNP residues 51-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: MDR_19A / Gene: SpneCM_010100000757, SP_0659 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97RX4, UniProt: A0A0H2UP26*PLUS, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% w/v PEG3350, 0.2 M magnesium chloride, 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 29395 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.054 / Net I/σ(I): 40.22
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.11 / Rsym value: 0.579 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H30

2h30


Resolution: 1.506→29.831 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 1419 4.97 %RANDOM
Rwork0.1689 ---
obs0.1703 29395 99.55 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.263 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0971 Å20 Å2-0 Å2
2--1.0971 Å20 Å2
3----2.1942 Å2
Refinement stepCycle: LAST / Resolution: 1.506→29.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 0 207 1301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131244
X-RAY DIFFRACTIONf_angle_d1.4361709
X-RAY DIFFRACTIONf_dihedral_angle_d13.819487
X-RAY DIFFRACTIONf_chiral_restr0.095189
X-RAY DIFFRACTIONf_plane_restr0.007220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.506-1.53320.2481330.23232565X-RAY DIFFRACTION94
1.5332-1.56270.25771460.2172761X-RAY DIFFRACTION100
1.5627-1.59460.22271440.20612755X-RAY DIFFRACTION100
1.5946-1.62930.2161430.19572776X-RAY DIFFRACTION100
1.6293-1.66720.24351450.2052774X-RAY DIFFRACTION100
1.6672-1.70890.26681430.19812749X-RAY DIFFRACTION100
1.7089-1.75510.231440.1852748X-RAY DIFFRACTION100
1.7551-1.80670.19241430.1762761X-RAY DIFFRACTION100
1.8067-1.8650.23061420.17092766X-RAY DIFFRACTION100
1.865-1.93170.2241440.17052739X-RAY DIFFRACTION100
1.9317-2.0090.22461410.17232746X-RAY DIFFRACTION100
2.009-2.10040.1921450.17542767X-RAY DIFFRACTION100
2.1004-2.21110.20791470.16862751X-RAY DIFFRACTION100
2.2111-2.34960.17811480.16172773X-RAY DIFFRACTION100
2.3496-2.53090.1781490.16452754X-RAY DIFFRACTION100
2.5309-2.78550.19321430.16292750X-RAY DIFFRACTION100
2.7855-3.18810.22991440.16662751X-RAY DIFFRACTION100
3.1881-4.01510.17531470.1582755X-RAY DIFFRACTION100
4.0151-29.83650.18051340.16272688X-RAY DIFFRACTION97
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)
16.36992.3923-1.43782.7442-0.36364.38740.189-0.7872-0.33620.527-0.4275-0.37730.47960.12580.17520.3272-0.05730.01360.22070.00180.143722.444153.260748.7657
23.67281.2857-1.01562.9394-0.70933.63560.0423-0.00610.21110.2171-0.07010.30620.0171-0.19380.01580.13160.00530.04320.0982-0.030.136119.20154.201134.722
35.46281.9654-0.20223.70810.3162.19260.1001-0.2036-0.35270.2605-0.14840.03870.3799-0.14360.06140.2183-0.00460.02030.1150.00870.101318.125644.036938.2443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 51:70
2X-RAY DIFFRACTION2chain A and resid 71:135
3X-RAY DIFFRACTION3chain A and resid 136:188

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