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- PDB-1y7y: High-resolution crystal structure of the restriction-modification... -

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Basic information

Entry
Database: PDB / ID: 1y7y
TitleHigh-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila
ComponentsC.AhdI
KeywordsTranscription regulator / HELIX-TURN-HELIX / DNA-BINDING PROTEIN / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsMcGeehan, J.E. / Streeter, S.D. / Papapanagiotou, I. / Fox, G.C. / Kneale, G.G.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.
Authors: McGeehan, J.E. / Streeter, S.D. / Papapanagiotou, I. / Fox, G.C. / Kneale, G.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia
Authors: McGeehan, J.E. / Streeter, S. / Cooper, J.B. / Mohammed, F. / Fox, G.C. / Kneale, G.G.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C.AhdI
B: C.AhdI


Theoretical massNumber of molelcules
Total (without water)16,7652
Polymers16,7652
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-15 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.403, 57.246, 46.125
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS WHICH MAKE UP THE BIOLOGICAL DIMER

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Components

#1: Protein C.AhdI


Mass: 8382.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q7X0F0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, IMIDAZOLE-MALATE, 2-METHYL-2,4-PENTANEDIOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.904989 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2003 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.904989 Å / Relative weight: 1
ReflectionResolution: 1.66→45.57 Å / Num. all: 14937 / Num. obs: 14302 / % possible obs: 95.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 8
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1561 / Rsym value: 0.181 / % possible all: 95.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Mutant I58M of C.AhdI, SeMet MAD to 2.5A

Resolution: 1.69→18.4 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 674 4.8 %RANDOM
Rwork0.169 ---
all0.169 14059 --
obs-14058 --
Refinement stepCycle: LAST / Resolution: 1.69→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 0 147 1217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.018
X-RAY DIFFRACTIONr_angle_refined_deg1.524

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