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- PDB-3fac: Crystal structure of Rhodobacter sphaeroides protein RSP_2168. No... -

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Basic information

Entry
Database: PDB / ID: 3fac
TitleCrystal structure of Rhodobacter sphaeroides protein RSP_2168. Northeast Structural Genomics target RhR83.
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Rhodobacter sphaeroides / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


carbon-sulfur lyase activity / metal ion binding
Similarity search - Function
Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A - #70 / CENP-V/GFA domain / Glutathione-dependent formaldehyde-activating enzyme / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
GFA domain-containing protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Neely, H. / Forouhar, F. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Neely, H. / Forouhar, F. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionNov 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein
G: Putative uncharacterized protein
H: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)106,1608
Polymers106,1608
Non-polymers00
Water5,909328
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,2701
Polymers13,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.579, 125.996, 135.791
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 uncharacterized protein


Mass: 13269.985 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Gene: RHOS4_07510, RSP_2168 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J4G5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M NH4Cl, 10% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 76051 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.091 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 9.2 / Num. unique all: 7772 / Rsym value: 0.25 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 51948.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2494 3.4 %RANDOM
Rwork0.225 ---
obs0.225 72474 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5015 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.76 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 0 328 7171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 419 3.5 %
Rwork0.298 11575 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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