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- PDB-1t6s: Crystal structure of a conserved hypothetical protein from Chloro... -

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Basic information

Entry
Database: PDB / ID: 1t6s
TitleCrystal structure of a conserved hypothetical protein from Chlorobium tepidum
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / a winged helix-turn-helix / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


chromosome separation / cell division / cytoplasm
Similarity search - Function
Chromosome segregation/condensation protein ScpB / Segregation and condensation complex subunit ScpB / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Segregation and condensation protein B
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKim, J.S. / Shin, D.H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning.
Authors: Kim, J.S. / Shin, D.H. / Pufan, R. / Huang, C. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25623
Polymers36,9542
Non-polymers1,30221
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-1 kcal/mol
Surface area19380 Å2
MethodPISA
2
A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,51246
Polymers73,9084
Non-polymers2,60442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area20810 Å2
ΔGint-40 kcal/mol
Surface area30910 Å2
MethodPISA
3
A: conserved hypothetical protein
hetero molecules

B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25623
Polymers36,9542
Non-polymers1,30221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area5210 Å2
ΔGint-11 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.42, 69.42, 117.99
Angle α, β, γ (deg.)90, 90, 120
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-467-

HOH

DetailsBiological assembly is a dimer in the assymmetric unit.

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Components

#1: Protein conserved hypothetical protein


Mass: 18476.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Plasmid: pB3.1371B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q8KF54
#2: Chemical...
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.195 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium nitrate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2004 / Details: W16 wiggler
RadiationMonochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→500 Å / Num. all: 23372 / Num. obs: 23532 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Rsym value: 0.03 / Net I/σ(I): 11.6
Reflection shellResolution: 1.95→1.98 Å / Rsym value: 0.491 / % possible all: 95.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2531 1064 random
Rwork0.2157 --
all0.23 23484 -
obs0.23 22062 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.75 Å2-1.798 Å20 Å2
2---2.75 Å20 Å2
3---5.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 84 98 2786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.24
LS refinement shellResolution: 1.95→1.98 Å
RfactorNum. reflection% reflection
Rfree0.3058 45 -
Rwork0.3086 --
obs-842 90.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3no3.param

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