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- PDB-1rfz: Structure of Protein of Unknown Function from Bacillus stearother... -

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Basic information

Entry
Database: PDB / ID: 1rfz
TitleStructure of Protein of Unknown Function from Bacillus stearothermophilus
ComponentsHypothetical protein APC35681
KeywordsStructural Genomics / unknown function / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphatidylglycerophosphatase activity / lipid metabolic process
Similarity search - Function
YutG-like / PgpA-like / YutG/PgpA domain / Putative phosphatidylglycerophosphatase / PgpA-like superfamily / Phosphatidylglycerophosphatase A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKim, Y. / Wu, R. / Cuff, M.E. / Quartey, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of hypothetical protein APC35681 from Bacillus stearothermophilus
Authors: Kim, Y. / Wu, R. / Cuff, M.E. / Quartey, P. / Joachimiak, A.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE THERE WAS NO DATABASE REFERENCE SEQUENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. ...SEQUENCE THERE WAS NO DATABASE REFERENCE SEQUENCE FOR THE PROTEIN AT THE TIME OF PROCESSING. RESIDUES -2 TO 0 ARE CLONING ARTIFACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein APC35681
B: Hypothetical protein APC35681
C: Hypothetical protein APC35681
D: Hypothetical protein APC35681
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,62811
Polymers75,9564
Non-polymers6727
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-159 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.824, 80.824, 236.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-425-

HOH

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Components

#1: Protein
Hypothetical protein APC35681


Mass: 18988.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: P84133
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956, 0.97943, 0.9647
DetectorType: SBC-2 / Detector: CCD / Date: Feb 6, 2003 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.979431
30.96471
ReflectionResolution: 2.7→47.7 Å / Num. all: 22606 / Num. obs: 22606 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 15 % / Rmerge(I) obs: 0.792 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 287184.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1951 9.9 %RANDOM
Rwork0.221 ---
obs0.221 19716 97.5 %-
all-19716 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4785 Å2 / ksol: 0.341003 e/Å3
Displacement parametersBiso mean: 66.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.79 Å20 Å20 Å2
2--5.79 Å20 Å2
3----11.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 35 117 5264
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.812
X-RAY DIFFRACTIONc_scbond_it3.732
X-RAY DIFFRACTIONc_scangle_it6.212.5
LS refinement shellResolution: 2.8→2.93 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.402 383 8.8 %
Rwork0.324 3945 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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