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- PDB-2o8s: X-ray Crystal Structure of Protein AGR_C_984 from Agrobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2o8s
TitleX-ray Crystal Structure of Protein AGR_C_984 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR120.
ComponentsAGR_C_984p
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / all alpha-helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyAGR_C_984p-like / AGR C 984p-like / Protein of unknown function DUF1217 / AGR-C-984p-like superfamily / Protein of unknown function (DUF1217) / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSeetharaman, J. / Forouhar, F. / Su, M. / Zhao, L. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Forouhar, F. / Su, M. / Zhao, L. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein AGR_C_984 from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR120.
Authors: Seetharaman, J. / Forouhar, F. / Su, M. / Zhao, L. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGR_C_984p
B: AGR_C_984p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8364
Polymers70,6442
Non-polymers1922
Water86548
1
A: AGR_C_984p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4182
Polymers35,3221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGR_C_984p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4182
Polymers35,3221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.490, 42.490, 332.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein AGR_C_984p


Mass: 35321.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: locus_tag="AGR_C_984" / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7D182, UniProt: A0A0F4FZC1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 100mM CAPS, 40% PEG1k, 100mM ammonium sulfate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2006 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→29.73 Å / Num. all: 47420 / Num. obs: 46946 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.76 / Rsym value: 0.58 / Net I/σ(I): 18.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5540 / Rsym value: 0.325 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SOLVEphasing
XTALVIEWrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.73 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: The structure factors are twinned. Twinning operator : h, -k, -l, Twinning fraction : 0.459 waters picked at level greater than 3.0
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 3476 -RANDOM
Rwork0.2429 ---
all0.2428 47420 --
obs0.2428 37514 82.4 %-
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.949 Å20 Å20 Å2
2---3.949 Å20 Å2
3---7.898 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 10 48 3650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.282 1647 -
Rwork0.244 --
obs-4205 74.8 %

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