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- PDB-4qba: Crystal structure of the effector-binding domain of S. aureus CcpE -

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Basic information

Entry
Database: PDB / ID: 4qba
TitleCrystal structure of the effector-binding domain of S. aureus CcpE
ComponentsLysR family regulatory protein
KeywordsTRANSCRIPTION REGULATOR / LysR type transcriptional regulator
Function / homologyD-Maltodextrin-Binding Protein; domain 2 - #290 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsLiu, X. / Lan, L. / Yang, C.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Metabolic sensor governing bacterial virulence in Staphylococcus aureus.
Authors: Ding, Y. / Liu, X. / Chen, F. / Di, H. / Xu, B. / Zhou, L. / Deng, X. / Wu, M. / Yang, C.G. / Lan, L.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: LysR family regulatory protein
B: LysR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8684
Polymers47,7972
Non-polymers712
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-34 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.605, 77.182, 93.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 87 - 281 / Label seq-ID: 9 - 203

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein LysR family regulatory protein / CcpE


Mass: 23898.746 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 79-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: SAS0637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GBF8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 33% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9735 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25824 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.21→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.139 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.236 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24295 1372 5 %RANDOM
Rwork0.20241 ---
obs0.20449 25824 98.8 %-
all-25824 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.719 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-0 Å2-0 Å2
2--1.07 Å20 Å2
3----3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.21→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 2 67 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193294
X-RAY DIFFRACTIONr_bond_other_d0.0030.023113
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9624467
X-RAY DIFFRACTIONr_angle_other_deg0.93437168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30625.833168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6691510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213759
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02761
Refine LS restraints NCS

Ens-ID: 1 / Number: 11696 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.208→2.265 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 67 -
Rwork0.27 1791 -
obs--93.65 %

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