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- PDB-2oeb: The crystal structure of gene product Af1862 from Archaeoglobus f... -

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Basic information

Entry
Database: PDB / ID: 2oeb
TitleThe crystal structure of gene product Af1862 from Archaeoglobus fulgidus
ComponentsHypothetical protein
KeywordsStructural genomics / unknown function / Archaeoglobus fulgidus / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


defense response to virus / cytoplasm
Similarity search - Function
AF1862-like domain / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, Cmr5 / AF1862-like domain superfamily / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR system Cmr subunit Cmr5
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsZhang, R. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of gene product Af1862 from Archaeoglobus fulgidus
Authors: Zhang, R. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)17,4081
Polymers17,4081
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.309, 73.309, 147.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-158-

HOH

21A-184-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 17407.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: gene product Af_1862 from Archaeoglobus fulgidus / Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_1862 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28417
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium Acetate, 0.1M Na Citate, 30% PEG 2K MME, pH 5.6, 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: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.66→58.32 Å / Num. all: 17377 / Num. obs: 16823 / % possible obs: 96.81 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 39.02
Reflection shellResolution: 1.66→1.703 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.53 / Num. unique all: 1329 / % possible all: 93.23

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.66→58.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.65 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23358 914 5.2 %RANDOM
Rwork0.18514 ---
all0.18755 17377 --
obs0.18755 16823 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.66→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 149 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221224
X-RAY DIFFRACTIONr_bond_other_d0.0010.02834
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9651649
X-RAY DIFFRACTIONr_angle_other_deg0.87832052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5732655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.712152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined0.230.2304
X-RAY DIFFRACTIONr_nbd_other0.1720.2869
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2632
X-RAY DIFFRACTIONr_nbtor_other0.0860.2598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.213
X-RAY DIFFRACTIONr_mcbond_it1.4891.5987
X-RAY DIFFRACTIONr_mcbond_other0.4621.5307
X-RAY DIFFRACTIONr_mcangle_it1.77321209
X-RAY DIFFRACTIONr_scbond_it2.7763567
X-RAY DIFFRACTIONr_scangle_it3.8214.5440
X-RAY DIFFRACTIONr_rigid_bond_restr3.75532575
X-RAY DIFFRACTIONr_sphericity_free5.2643149
X-RAY DIFFRACTIONr_sphericity_bonded2.88632035
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 73 -
Rwork0.226 1166 -
obs-1239 93.23 %

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