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- PDB-2hly: The crystal structure of genomics APC5867 -

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Basic information

Entry
Database: PDB / ID: 2hly
TitleThe crystal structure of genomics APC5867
ComponentsHypothetical protein Atu2299
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ATC2257 / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Atu2299-like / Hypothetical protein Atu2299 / Protein of unknown function DUF2026 / Atu2299-like domain superfamily / Protein of unknown function (DUF2026) / Papain-like cysteine peptidase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DUF2026 domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / Sulfur SAD / Resolution: 1.6 Å
AuthorsDong, A. / Xu, X. / Zheng, H. / Kim, Y. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of genomics APC5867
Authors: Dong, A. / Xu, X. / Zheng, H. / Kim, Y. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Atu2299


Theoretical massNumber of molelcules
Total (without water)22,7721
Polymers22,7721
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.555, 50.391, 81.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein Atu2299 / AGR_C_4178p


Mass: 22771.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: p15Tv lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8UD29, UniProt: A9CI22*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 6
Details: 0.1M Bis-Tris pH 6.0, 1.5M Ammonium Sulphate, VAPOR DIFFUSION, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20012.29
ROTATING ANODERIGAKU21.54
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEApr 24, 2006VeriMax Cr
RIGAKU RAXIS IV++2IMAGE PLATEMay 10, 2006VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.291
21.541
ReflectionResolution: 1.6→50 Å / Num. all: 23511 / Num. obs: 23511 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 30
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.4 / Num. unique all: 690 / Rsym value: 0.1 / % possible all: 57

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: Sulfur SAD / Resolution: 1.6→42.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BOTH REFMAC AND COOT ARE USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.21352 748 3.2 %RANDOM
Rwork0.17313 ---
all0.17435 22713 --
obs0.17435 22713 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 0 279 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9292214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2525205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4223.10874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38315249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2231510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021274
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2779
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21125
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.51054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35821617
X-RAY DIFFRACTIONr_scbond_it2.033689
X-RAY DIFFRACTIONr_scangle_it3.0574.5597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 36 -
Rwork0.262 1029 -
obs--59.3 %

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