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- PDB-2qvo: Crystal structure of AF1382 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2qvo
TitleCrystal structure of AF1382 from Archaeoglobus fulgidus
ComponentsUncharacterized protein AF_1382
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF1382 / Archaeoglobus fulgidus / PSI / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG
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 DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 1.85 Å
AuthorsZhu, J. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Hao, X. / Chen, L. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structure of AF1382 from Archaeoglobus fulgidus.
Authors: Zhu, J. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Hao, X. / Chen, L. / Liu, Z.J. / Rose, J.P. / Wang, B.C.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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_565-x,-y+1,z1
Buried area2250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 53.033, 40.968
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-133-

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 DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: VC-16, JCM 9628, NBRC 100126 / 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.: 38 / 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 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 mg/ml) AND SOLUTION CONTAINING 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, 30% w/v POLYETHYLENE GLYCOL ...Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 mg/ml) AND SOLUTION CONTAINING 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, 30% w/v POLYETHYLENE GLYCOL MONOMETHYL ETHER, pH 4.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97240, 1.90000
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97241
21.91
ReflectionResolution: 1.85→50 Å / Num. obs: 19060 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rsym value: 0.051 / Net I/σ(I): 12.96
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 12.5 % / Rsym value: 0.233 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SGXPROmodel building
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: Sulfur SAD / Resolution: 1.85→37.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. Initial phases were obtained from sulfur phasing using data collected at wavelength 1.90000 A. Then the structure was refined using 0.9724 A - wavelength data and deposited in PDB. 2. The ...Details: 1. Initial phases were obtained from sulfur phasing using data collected at wavelength 1.90000 A. Then the structure was refined using 0.9724 A - wavelength data and deposited in PDB. 2. The Bijvoet differences were used for phasing. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27983 475 4.8 %RANDOM
Rwork0.23661 ---
obs0.23874 9373 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 0 38 752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022699
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.984935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.619586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.382526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48315142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.142152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02488
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7131.5431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3292699
X-RAY DIFFRACTIONr_scbond_it1.9943268
X-RAY DIFFRACTIONr_scangle_it3.1664.5236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 31 -
Rwork0.345 691 -
obs--99.72 %

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