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- PDB-2i5h: Crystal structure of Af1531 from Archaeoglobus fulgidus, Pfam DUF655 -

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Basic information

Entry
Database: PDB / ID: 2i5h
TitleCrystal structure of Af1531 from Archaeoglobus fulgidus, Pfam DUF655
ComponentsHypothetical protein AF1531
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein AF1531 / PFAM:DUF655 / PSI-2 / 10225b / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Protein of unknown function DUF655 / Protein of unknown function (DUF655) / AF1531-like domain / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DUF655 domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein AF1531 from Archaeoglobus fulgidus.
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: 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: Hypothetical protein AF1531


Theoretical massNumber of molelcules
Total (without water)24,4541
Polymers24,4541
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.730, 37.490, 85.250
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein AF1531


Mass: 24454.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O28741
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG MME 5000, 0.1M MES, 0.2M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.9791
SYNCHROTRONNSLS X12C21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDJun 5, 2006Si (111)
ADSC QUANTUM 2102CCDMay 12, 2006Si (111)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
211
ReflectionResolution: 1.74→31.8 Å / Num. all: 23465 / Num. obs: 23465 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 23.5
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.319 / Num. unique all: 1397 / % possible all: 56.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVE& SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→31.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed in remark 465 and Atoms listed in remark 470 were not modeled due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 892 -RANDOM
Rwork0.2279 ---
obs0.2279 22800 90.8 %-
all-22800 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.478 Å20 Å24.471 Å2
2--0.714 Å20 Å2
3---1.764 Å2
Refinement stepCycle: LAST / Resolution: 1.74→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 0 132 1589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.122

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