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- PDB-3huu: Crystal structure of transcription regulator like protein from St... -

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Basic information

Entry
Database: PDB / ID: 3huu
TitleCrystal structure of transcription regulator like protein from Staphylococcus haemolyticus
ComponentsTranscription regulator like protein
KeywordsTranscription regulator / PSI-II / NYSGXRC / 11235m / Lac I / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyPeriplasmic binding protein-like domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of transcription regulator like protein from Staphylococcus haemolyticus
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription regulator like protein
B: Transcription regulator like protein
C: Transcription regulator like protein
D: Transcription regulator like protein


Theoretical massNumber of molelcules
Total (without water)138,8174
Polymers138,8174
Non-polymers00
Water2,306128
1
A: Transcription regulator like protein
B: Transcription regulator like protein


Theoretical massNumber of molelcules
Total (without water)69,4082
Polymers69,4082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-10 kcal/mol
Surface area21180 Å2
MethodPISA
2
C: Transcription regulator like protein
D: Transcription regulator like protein


Theoretical massNumber of molelcules
Total (without water)69,4082
Polymers69,4082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-8 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.872, 68.080, 97.835
Angle α, β, γ (deg.)82.42, 75.95, 79.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcription regulator like protein / Similar to maltose operon transcriptional repressor


Mass: 34704.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Strain: JCSC1435 / Gene: SH1407 / Plasmid: pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q4L6K9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8K, 8% Ethylene Glycol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2009 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 82791 / Num. obs: 82791 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4504 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXD& SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 1.95→43.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 103598.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The missing residues and missing atoms are due to weak or no electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2336 3 %RANDOM
Rwork0.237 ---
all0.25 82791 --
obs0.237 77844 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5588 Å2 / ksol: 0.351416 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å2-1.85 Å2-9.93 Å2
2--0.16 Å21.67 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 0 128 8497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 374 3 %
Rwork0.276 11944 -
obs-82791 79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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