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- PDB-2ap6: X-Ray Crystal Structure of Protein Atu4242 from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 2ap6
TitleX-Ray Crystal Structure of Protein Atu4242 from Agrobacterium tumefaciens. Northeast Strucutral Genomics Consortium Target AtR43.
Componentshypothetical protein Atu4242
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG
Function / homology
Function and homology information


NIPSNAP / : / NIPSNAP / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NIPSNAP domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a Hypothetical protein Atu4242 from Agrobacterium tumefaciens (strain C58 / ATCC 3 NESG Target ATR43.
Authors: Benach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionAug 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Atu4242
B: hypothetical protein Atu4242
C: hypothetical protein Atu4242
D: hypothetical protein Atu4242
E: hypothetical protein Atu4242
F: hypothetical protein Atu4242
G: hypothetical protein Atu4242
H: hypothetical protein Atu4242


Theoretical massNumber of molelcules
Total (without water)107,5598
Polymers107,5598
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20340 Å2
ΔGint-111 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.832, 134.830, 56.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
hypothetical protein Atu4242 / AGR_L_1239p


Mass: 13444.924 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu4242 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U857, UniProt: A9CGA4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.41 Å3/Da / Density % sol: 49.12 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 61871 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.17
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.28 / % possible all: 86.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
COMOphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1VQS

1vqs


Resolution: 2.5→19.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259473.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 1820 3.1 %RANDOM
Rwork0.1965 ---
obs0.1965 58711 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.6857 Å2 / ksol: 0.390826 e/Å3
Displacement parametersBiso mean: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å20 Å2
2--0.9 Å20 Å2
3---2.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 0 184 7048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 143 1.6 %
Rwork0.335 8774 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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