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- PDB-5d1i: Structure of Cyclic nucleotide-binding-like protein from Brucella... -

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Basic information

Entry
Database: PDB / ID: 5d1i
TitleStructure of Cyclic nucleotide-binding-like protein from Brucella abortus bv. 1 str. 9-941
ComponentsCyclic nucleotide-binding protein
KeywordsUNKNOWN FUNCTION / beta barrel
Function / homology
Function and homology information


DNA-binding transcription factor activity / cytosol
Similarity search - Function
: / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclic nucleotide-binding protein
Similarity search - Component
Biological speciesBrucella abortus biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHe, Z. / Dong, J. / Li, X. / Gao, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of cyclic nucleotide-binding-like protein from Brucella abortus
Authors: He, Z. / Gao, Y. / Dong, J. / Ke, Y. / Li, X. / Chen, Z. / Zhang, X.C.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic nucleotide-binding protein
B: Cyclic nucleotide-binding protein


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,9102
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.096, 82.911, 103.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-291-

HOH

21B-256-

HOH

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Components

#1: Protein Cyclic nucleotide-binding protein


Mass: 14455.212 Da / Num. of mol.: 2 / Fragment: UNP residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus biovar 1 (bacteria) / Strain: 9-941 / Gene: BruAb1_1980 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57AQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Potassium sodium tartrate tetrahydrate,olyethylene glycol 3350, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2015 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16773 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 20.38 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.016 / Rrim(I) all: 0.087 / Χ2: 1.091 / Net I/av σ(I): 45.157 / Net I/σ(I): 11.9 / Num. measured all: 478013
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.07150.38116370.9920.0720.3881.126100
2.07-2.1529.20.29916460.9950.0560.3041.091100
2.15-2.2529.20.24716460.9950.0460.2521.084100
2.25-2.3729.10.19316630.9970.0360.1961.046100
2.37-2.5229.20.15916540.9980.030.1621.03100
2.52-2.71290.13216640.9980.0250.1351.071100
2.71-2.9928.70.10616840.9990.020.1081.055100
2.99-3.4227.90.08516760.9990.0170.0871.059100
3.42-4.31270.06817190.9990.0130.071.123100
4.31-5026.70.05417840.9980.0110.0551.23399.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: -0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0
Phasing dmFOM : 0.72 / FOM acentric: 0.72 / FOM centric: 0.73 / Reflection: 16673 / Reflection acentric: 14856 / Reflection centric: 1817
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-500.930.950.9789569220
3.6-5.70.950.960.9122951938357
2.8-3.60.890.890.8428442511333
2.5-2.80.760.770.6828132536277
2.1-2.50.620.620.5849894569420
2-2.10.440.450.4229432733210

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHASESphasing
RESOLVE2.15model building
PHENIXdev_1819refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→24.682 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 833 5 %Random selection
Rwork0.1853 15832 --
obs0.1877 16665 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.9 Å2 / Biso mean: 28.1482 Å2 / Biso min: 7.66 Å2
Refinement stepCycle: final / Resolution: 2→24.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 171 1969
Biso mean---36.06 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041818
X-RAY DIFFRACTIONf_angle_d0.7282456
X-RAY DIFFRACTIONf_chiral_restr0.025296
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d14.619678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9953-2.12030.29241310.21632496X-RAY DIFFRACTION95
2.1203-2.28390.27221370.21012593X-RAY DIFFRACTION99
2.2839-2.51350.26121380.21482628X-RAY DIFFRACTION99
2.5135-2.87670.24461400.20912657X-RAY DIFFRACTION100
2.8767-3.62260.24331410.18032676X-RAY DIFFRACTION100
3.6226-100.1821460.15312782X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.5412 Å / Origin y: 42.524 Å / Origin z: 26.3433 Å
111213212223313233
T0.1054 Å20.003 Å20.0213 Å2-0.0598 Å2-0.0103 Å2--0.1435 Å2
L2.4095 °20.382 °20.3612 °2-2.4567 °20.1667 °2--1.3259 °2
S-0.0043 Å °0.0446 Å °-0.0574 Å °-0.2268 Å °-0.0448 Å °-0.2214 Å °-0.0313 Å °-0.0526 Å °0.0386 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 118
2X-RAY DIFFRACTION1allB4 - 119
3X-RAY DIFFRACTION1allA201 - 298
4X-RAY DIFFRACTION1allB201 - 273

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