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- PDB-3o3k: Crystal structure of AF1382 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 3o3k
TitleCrystal structure of AF1382 from Archaeoglobus fulgidus
ComponentsUncharacterized protein AF_1382
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Southeast Collaboratory for Structural Genomics / sulfur phasing / SECSG / Protein Structure Initiative
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein AF_1382
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 2.3 Å
AuthorsZhu, J.-Y. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Xu, H. / Chen, L. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.
Authors: Zhu, J.Y. / Fu, Z.Q. / Chen, L. / Xu, H. / Chrzas, J. / Rose, J. / Wang, B.C.
History
DepositionJul 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 4, 2012Group: Database references
Revision 1.3Sep 19, 2012Group: Database references
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: Uncharacterized protein AF_1382


Theoretical massNumber of molelcules
Total (without water)11,1591
Polymers11,1591
Non-polymers00
Water57632
1
A: Uncharacterized protein AF_1382

A: Uncharacterized protein AF_1382


Theoretical massNumber of molelcules
Total (without water)22,3182
Polymers22,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area2210 Å2
ΔGint-18 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.540, 53.540, 41.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-97-

HOH

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Components

#1: Protein Uncharacterized protein AF_1382


Mass: 11159.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1382 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RPX / References: UniProt: O28889
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: THE LAST REPRESENTS MERGED DATA SET
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.5
Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 MG/ML) AND SOLUTION CONTAING 0.1M SODIUM CITRATE/CITRIC ACID PH 5.5, 0.1M SODIUM CHLORIDE, 0.1M LITHIUM ...Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 MG/ML) AND SOLUTION CONTAING 0.1M SODIUM CITRATE/CITRIC ACID PH 5.5, 0.1M SODIUM CHLORIDE, 0.1M LITHIUM SULPHATE, 30% V/V PEG 400, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 5325 / % possible obs: 99.9 % / Redundancy: 25 % / Biso Wilson estimate: 37.5 Å2 / Rsym value: 0.045 / Net I/σ(I): 124.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 17.4 / Num. unique all: 5325 / Rsym value: 0.254 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SGXPROmodel building
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: Sulfur SAD / Resolution: 2.3→37.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 160315.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 536 5.3 %RANDOM
Rwork0.232 ---
obs0.232 5325 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7117 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 0 32 772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.922.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 88 5.3 %
Rwork0.327 1558 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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