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- PDB-3l78: The crystal structure of SMU.1142C from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l78
TitleThe crystal structure of SMU.1142C from Streptococcus mutans UA159
ComponentsRegulatory protein spx
KeywordsTRANSCRIPTION / transcriptional factor / STREPTOCOCCUS MUTANS / Disulfide bond / Redox-active center / Transcription regulation
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Global transcriptional regulator Spx
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, X. / Fu, T.M. / Su, X.-D.
CitationJournal: To be Published
Title: The crystal structure of SMU.1142c from Streptococcus mutans UA159
Authors: Liu, X. / Fu, T.M. / Su, X.-D.
History
DepositionDec 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein spx


Theoretical massNumber of molelcules
Total (without water)14,0471
Polymers14,0471
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.565, 47.473, 56.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulatory protein spx / putative transcriptional factor SpxA


Mass: 14047.194 Da / Num. of mol.: 1 / Fragment: residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.1142c (AMINO ACIDS 1-120) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DU17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.85 NaNO3, 0.1M NaCAD pH 6.5, 15% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 10132 / Num. obs: 9865 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Χ2: 1.064 / Net I/av σ(I): 51.994 / Net I/σ(I): 10.7 / Num. measured all: 134385
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.938.80.3194870.50298.8
1.93-1.979.70.3054770.6599.8
1.97-2.01110.2874940.532100
2.01-2.0511.80.2375060.578100
2.05-2.0912.60.1944940.64699.8
2.09-2.1413.20.194980.67100
2.14-2.1913.60.1725000.698100
2.19-2.2514.20.1594980.727100
2.25-2.3214.30.1414840.746100
2.32-2.3914.40.1285210.798100
2.39-2.4814.60.1194920.804100
2.48-2.5814.40.1054980.846100
2.58-2.714.40.0995110.936100
2.7-2.8414.40.0865061.052100
2.84-3.0214.50.0765061.164100
3.02-3.2514.40.0645121.4100
3.25-3.5814.20.0585101.644100
3.58-4.0914.10.0525311.906100
4.09-5.1613.80.055282.165100
5.16-5012.30.0495792.03499.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z3E

1z3e


Resolution: 1.9→36.318 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU ML: 0.29 / σ(F): 0.1 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1000 10.18 %
Rwork0.1864 8828 -
obs0.1909 9828 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.454 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 86.04 Å2 / Biso mean: 33.022 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.068 Å20 Å2-0 Å2
2--8.912 Å20 Å2
3----7.844 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 0 46 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004972
X-RAY DIFFRACTIONf_angle_d0.8131317
X-RAY DIFFRACTIONf_dihedral_angle_d15.555375
X-RAY DIFFRACTIONf_chiral_restr0.056155
X-RAY DIFFRACTIONf_plane_restr0.003171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.28771390.19231158X-RAY DIFFRACTION93
2.0002-2.12550.24041330.16431217X-RAY DIFFRACTION96
2.1255-2.28960.20181420.16031235X-RAY DIFFRACTION96
2.2896-2.51990.23661400.17191255X-RAY DIFFRACTION98
2.5199-2.88440.24611400.20621283X-RAY DIFFRACTION99
2.8844-3.63350.26341510.18831300X-RAY DIFFRACTION99
3.6335-36.32510.2021550.18581380X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.834 Å / Origin y: -5.784 Å / Origin z: 3.793 Å
111213212223313233
T0.1273 Å2-0.0021 Å2-0.0081 Å2-0.1431 Å20.0053 Å2--0.1188 Å2
L0.6367 °2-0.301 °20.198 °2-0.6599 °20.0859 °2---0.0203 °2
S-0.0925 Å °-0.0775 Å °-0.0351 Å °0.059 Å °0.0459 Å °0.0214 Å °-0.0929 Å °0.0332 Å °0.0306 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 117
2X-RAY DIFFRACTION1allA1 - 167

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