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- PDB-1w8i: The Structure of gene product af1683 from Archaeoglobus fulgidus. -

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Basic information

Entry
Database: PDB / ID: 1w8i
TitleThe Structure of gene product af1683 from Archaeoglobus fulgidus.
ComponentsPUTATIVE VAPC RIBONUCLEASE AF_1683
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ARCHAEOGLOBUS FULGIDUS / HYPOTHETICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


rRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Endonuclease VapC20 / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
VapC ribonuclease AF_1683
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsMidwest Center for Structural Genomics (MCSG) / Cuff, M.E. / Zhang, R. / Ginell, S.L. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
CitationJournal: To be Published
Title: The Structure of Gene Product Af1683 from Archaeoglobus Fulgidus
Authors: Cuff, M.E. / Zhang, R. / Ginell, S.L. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE VAPC RIBONUCLEASE AF_1683


Theoretical massNumber of molelcules
Total (without water)17,9601
Polymers17,9601
Non-polymers00
Water2,558142
1
A: PUTATIVE VAPC RIBONUCLEASE AF_1683

A: PUTATIVE VAPC RIBONUCLEASE AF_1683


Theoretical massNumber of molelcules
Total (without water)35,9212
Polymers35,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area2400 Å2
ΔGint-12.9 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.730, 66.730, 181.381
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

21A-2077-

HOH

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Components

#1: Protein PUTATIVE VAPC RIBONUCLEASE AF_1683 / HYPOTHETICAL PROTEIN AF1683 / PUTATIVE TOXIN AF_1683 / PUTATIVE RNASE AF_1683


Mass: 17960.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GENE PRODUCT AF1683 FROM ARCHAEOGLOBUS FULGIDUS / Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: DSM 4304 / Plasmid: P11 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O28590, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growpH: 5.5 / Details: SODIUM CITRATE, PEG 3350, GLYCEROL, pH 5.50

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97967, 0.97954
DetectorType: CUSTOM- SBC2 / Detector: CCD / Date: Apr 19, 2004 / Details: DUAL SLITS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979671
20.979541
ReflectionResolution: 2.1→50 Å / Num. obs: 26396 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
DMmodel building
HKL-2000data reduction
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
ARP/wARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→57.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.013 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 742 5 %RANDOM
Rwork0.211 ---
obs0.212 13960 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→57.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 0 142 1399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221282
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9671727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8623.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67315239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.894158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2577
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2896
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.5793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37921238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3283561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4634.5489
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 54 -
Rwork0.229 1010 -
obs--99.72 %

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