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- PDB-2zds: Crystal Structure of SCO6571 from Streptomyces coelicolor A3(2) -

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Basic information

Entry
Database: PDB / ID: 2zds
TitleCrystal Structure of SCO6571 from Streptomyces coelicolor A3(2)
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / TIM-barrel fold / DNA-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homologyDivalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / DNA binding / Alpha Beta / Putative DNA-binding protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBegum, P. / Gao, Y.G. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Protein Pept.Lett. / Year: 2008
Title: Crystal structure of SCO6571 from Streptomyces coelicolor A3(2).
Authors: Begum, P. / Sakai, N. / Hayashi, T. / Gao, Y.G. / Tamura, T. / Watanabe, N. / Yao, M. / Tanaka, I.
History
DepositionNov 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein
C: Putative DNA-binding protein
D: Putative DNA-binding protein
E: Putative DNA-binding protein
F: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)233,8066
Polymers233,8066
Non-polymers00
Water22,1401229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23250 Å2
ΔGint-116 kcal/mol
Surface area61050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.481, 171.593, 184.796
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
Putative DNA-binding protein


Mass: 38967.598 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: sco6571 / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: UniProt: O69946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 25% PEG 3350, 250mM sodium tartarate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.3→43.053 Å / Num. all: 120518 / Num. obs: 120397 / % possible obs: 99.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Biso Wilson estimate: 24.737 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.1 / Num. unique all: 11831 / Rsym value: 0.207 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 114274 -RANDOM
Rwork0.167 ---
obs0.167 114274 99.58 %-
all-114755 --
Displacement parametersBiso mean: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.188 Å0.229 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 0 1229 16757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_angle_refined_deg1.921
X-RAY DIFFRACTIONr_nbd_refined0.2
X-RAY DIFFRACTIONr_gen_planes_refined0.02
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2
X-RAY DIFFRACTIONr_mcbond_it1.5
X-RAY DIFFRACTIONr_mcangle_it2
X-RAY DIFFRACTIONr_scbond_it3
X-RAY DIFFRACTIONr_scangle_it4.5
X-RAY DIFFRACTIONr_nbtor_refined0.2
LS refinement shellResolution: 2.3→2.35 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.252 404 -
Rwork0.168 --
obs-8320 94.64 %

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