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- PDB-3l7q: Crystal structure of AldR from streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3l7q
TitleCrystal structure of AldR from streptococcus mutans
ComponentsPutative translation initiation inhibitor, aldR regulator-like protein
KeywordsTRANSLATION / aldR / streptococcus mutans / translation initiation inhibitor / regulator-like
Function / homology
Function and homology information


RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative translation initiation inhibitor aldR regulator-like protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFan, X.X. / Wang, K.T. / Su, X.D.
CitationJournal: To be Published
Title: Crystal structure of AldR from streptococcus mutans
Authors: Fan, X.X. / Wang, K.T. / Su, X.D.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative translation initiation inhibitor, aldR regulator-like protein
B: Putative translation initiation inhibitor, aldR regulator-like protein
C: Putative translation initiation inhibitor, aldR regulator-like protein
D: Putative translation initiation inhibitor, aldR regulator-like protein
E: Putative translation initiation inhibitor, aldR regulator-like protein
F: Putative translation initiation inhibitor, aldR regulator-like protein
G: Putative translation initiation inhibitor, aldR regulator-like protein
H: Putative translation initiation inhibitor, aldR regulator-like protein
I: Putative translation initiation inhibitor, aldR regulator-like protein


Theoretical massNumber of molelcules
Total (without water)122,1619
Polymers122,1619
Non-polymers00
Water4,143230
1
A: Putative translation initiation inhibitor, aldR regulator-like protein
B: Putative translation initiation inhibitor, aldR regulator-like protein
C: Putative translation initiation inhibitor, aldR regulator-like protein


Theoretical massNumber of molelcules
Total (without water)40,7203
Polymers40,7203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-29 kcal/mol
Surface area14820 Å2
MethodPISA
2
D: Putative translation initiation inhibitor, aldR regulator-like protein
E: Putative translation initiation inhibitor, aldR regulator-like protein
F: Putative translation initiation inhibitor, aldR regulator-like protein


Theoretical massNumber of molelcules
Total (without water)40,7203
Polymers40,7203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-29 kcal/mol
Surface area14920 Å2
MethodPISA
3
G: Putative translation initiation inhibitor, aldR regulator-like protein
H: Putative translation initiation inhibitor, aldR regulator-like protein
I: Putative translation initiation inhibitor, aldR regulator-like protein


Theoretical massNumber of molelcules
Total (without water)40,7203
Polymers40,7203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-29 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.124, 78.182, 102.488
Angle α, β, γ (deg.)90.00, 121.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative translation initiation inhibitor, aldR regulator-like protein


Mass: 13573.486 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: aldR, SMU_1308 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DTM5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.2M MgCl2, 0.1M Tris-HCl pH8.5, 25.0% PEG3350, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 40206 / Num. obs: 40167 / % possible obs: 99.9 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QD9

1qd9


Resolution: 2.5→41.37 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.549 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.925 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24974 2008 5 %RANDOM
Rwork0.21477 ---
obs0.21651 38109 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.097 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å2-1.7 Å2
2---0.26 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8532 0 0 230 8762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228685
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.97211826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.44851107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54726.154351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.501151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6681518
X-RAY DIFFRACTIONr_chiral_restr0.1030.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216435
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.55580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98729126
X-RAY DIFFRACTIONr_scbond_it2.86233105
X-RAY DIFFRACTIONr_scangle_it4.7654.52700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 156 -
Rwork0.29 2771 -
obs--99.73 %

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