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- PDB-7e5w: The structure of CcpA from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7e5w
TitleThe structure of CcpA from Staphylococcus aureus
ComponentsCatabolite control protein A
KeywordsDNA BINDING PROTEIN / dimer / regulater
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Catabolite control protein A / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Catabolite control protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsYu, G. / Wei, X.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Regulation of DNA-binding activity of the Staphylococcus aureus catabolite control protein A by copper (II)-mediated oxidation.
Authors: Liao, X. / Li, H. / Guo, Y. / Yang, F. / Chen, Y. / He, X. / Li, H. / Xia, W. / Mao, Z.W. / Sun, H.
History
DepositionFeb 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catabolite control protein A
B: Catabolite control protein A
C: Catabolite control protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8869
Polymers108,3103
Non-polymers5766
Water27015
1
A: Catabolite control protein A
hetero molecules

A: Catabolite control protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7838
Polymers72,2062
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5590 Å2
ΔGint-83 kcal/mol
Surface area24990 Å2
MethodPISA
2
B: Catabolite control protein A
C: Catabolite control protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4955
Polymers72,2062
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-49 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.287, 179.287, 173.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Catabolite control protein A /


Mass: 36103.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: ccpA, SA1557
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P99175
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: (NH4)2SO4, NaOAC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→42.3 Å / Num. obs: 46268 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 59.3 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.54-2.6913.60.5742130.9330.160.5920.519100
2.69-2.813.70.41442130.9690.1160.430.585100
2.8-2.9313.50.32542310.9710.0910.3380.664100
2.93-3.0812.60.24742070.9780.0720.2580.794100
3.08-3.2813.80.19342560.9880.0540.21.022100
3.28-3.5313.50.15542520.9910.0440.1611.308100
3.53-3.8812.70.1342670.9910.0380.1361.647100
3.88-4.4513.50.11643080.9940.0330.1212.032100
4.45-5.612.90.10643220.9940.0310.112.152100
5.6-6.512.20.09445170.9960.0290.0992.75199.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rzr

1rzr


Resolution: 2.55→42.26 Å / SU ML: 0.3251 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 2318 5.01 %
Rwork0.2331 43950 -
obs0.2342 46268 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.43 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 30 16 7417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00987482
X-RAY DIFFRACTIONf_angle_d1.292410106
X-RAY DIFFRACTIONf_chiral_restr0.08371189
X-RAY DIFFRACTIONf_plane_restr0.0061306
X-RAY DIFFRACTIONf_dihedral_angle_d18.35282834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60.3941050.392608X-RAY DIFFRACTION99.93
2.66-2.720.35041120.34312555X-RAY DIFFRACTION99.89
2.72-2.780.33281230.32022579X-RAY DIFFRACTION99.96
2.78-2.860.30181510.30042508X-RAY DIFFRACTION99.89
2.86-2.940.32691220.30352590X-RAY DIFFRACTION99.93
3.04-3.150.34961590.30762549X-RAY DIFFRACTION99.96
3.15-3.270.30771370.28572567X-RAY DIFFRACTION100
3.27-3.420.28931390.2692566X-RAY DIFFRACTION100
3.42-3.60.30851630.24022544X-RAY DIFFRACTION100
3.6-3.830.27391630.22882561X-RAY DIFFRACTION100
3.83-4.120.22881510.2082572X-RAY DIFFRACTION99.96
4.12-4.540.2214960.17482647X-RAY DIFFRACTION99.96
4.54-5.190.21081330.1842628X-RAY DIFFRACTION99.96
5.19-6.540.22911510.22752625X-RAY DIFFRACTION99.93

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