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- PDB-2a9s: The crystal structure of competence/damage inducible protein CihA... -

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Basic information

Entry
Database: PDB / ID: 2a9s
TitleThe crystal structure of competence/damage inducible protein CihA from Agrobacterium tumefaciens
Componentscompetence/damage-inducible protein CinA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC5759 / ATC1417 / MCSG / competence / damage inducible / Protein Structure Initiative / Midwest Center for Structural Genomics / PSI
Function / homology
Function and homology information


CinA-like / CinA, C-terminal / CinA-like, C-terminal / : / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Nicotinamide-nucleotide amidohydrolase PncC
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsLunin, V.V. / Evdokimova, E. / Kudritska, M. / Kim, Y. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of competence/damage inducible protein CihA from Agrobacterium tumefaciens
Authors: Lunin, V.V. / Evdokimova, E. / Kudritska, M. / Kim, Y. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: competence/damage-inducible protein CinA
B: competence/damage-inducible protein CinA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6614
Polymers35,5912
Non-polymers712
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-29 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.050, 68.790, 96.670
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 competence/damage-inducible protein CinA


Mass: 17795.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Plasmid: modified PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: GenBank: 17935342, UniProt: A9CJ26*PLUS
#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.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% isopropanol, 22% PEG 4K, 0.1M tris-Na Citrate dihydrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 29279 / Num. obs: 29279 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.087 / Net I/σ(I): 6.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.3 % / Num. unique all: 5678 / Rsym value: 0.732 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→48.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.497 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21869 1304 5.1 %RANDOM
Rwork0.16804 ---
all0.17066 24435 --
obs0.17066 24435 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 2 273 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222526
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9653432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94422.24598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551525
X-RAY DIFFRACTIONr_chiral_restr0.0890.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021887
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21279
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21752
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9551.51704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52822644
X-RAY DIFFRACTIONr_scbond_it2.5293900
X-RAY DIFFRACTIONr_scangle_it3.9594.5782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 84 -
Rwork0.228 1544 -
obs--100 %

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