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- PDB-2q00: Crystal structure of the P95883_SULSO protein from Sulfolobus sol... -

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Basic information

Entry
Database: PDB / ID: 2q00
TitleCrystal structure of the P95883_SULSO protein from Sulfolobus solfataricus. NESG target SsR10.
ComponentsOrf c02003 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / P95883 / NESG / SSO2109 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyArchaeal PaREP1 / Archaeal PaREP1/PaREP8 family / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Orf c02003 protein
Function and homology information
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Owens, L. / Ma, L.-C. / Cunningham, K. / Fang, Y. / Xiao, R. / Acton, T.B. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Owens, L. / Ma, L.-C. / Cunningham, K. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the P95883_SULSO protein from Sulfolobus solfataricus.
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Owens, L. / Ma, L.-C. / Cunningham, K. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orf c02003 protein
B: Orf c02003 protein


Theoretical massNumber of molelcules
Total (without water)30,1682
Polymers30,1682
Non-polymers00
Water52229
1
A: Orf c02003 protein


Theoretical massNumber of molelcules
Total (without water)15,0841
Polymers15,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Orf c02003 protein


Theoretical massNumber of molelcules
Total (without water)15,0841
Polymers15,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.927, 87.927, 176.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Orf c02003 protein


Mass: 15084.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Species: Sulfolobus solfataricus / Strain: P2, DSM 1617, JCM 11322 / Gene: orf c02003, SSO2109 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P95883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: 20 % PEG 4000, 0.1 M Ammonium thiocyanate, 0.1 M MES, pH 6.0, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 25384 / Num. obs: 25384 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5179 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→36.03 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 418136.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.265 868 4 %RANDOM
Rwork0.225 ---
obs0.225 21798 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.509 Å2 / ksol: 0.30844 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.18 Å20 Å20 Å2
2--6.18 Å20 Å2
3----12.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 0 29 1942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 129 4.7 %
Rwork0.251 2627 -
obs--64.3 %
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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