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- PDB-2gmy: Crystal Structure of a Protein of Unknown Function ATU0492 from A... -

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Basic information

Entry
Database: PDB / ID: 2gmy
TitleCrystal Structure of a Protein of Unknown Function ATU0492 from Agrobacterium tumefaciens, Putative Antioxidant Defence Protein AhpD
ComponentsHypothetical protein Atu0492
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a hypothetical protein Atu0492 from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionApr 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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 / 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: Hypothetical protein Atu0492
B: Hypothetical protein Atu0492
C: Hypothetical protein Atu0492
D: Hypothetical protein Atu0492
E: Hypothetical protein Atu0492
F: Hypothetical protein Atu0492


Theoretical massNumber of molelcules
Total (without water)102,8076
Polymers102,8076
Non-polymers00
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-116 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.009, 75.009, 148.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a hexamer. The deposited molecules A,B,C,D,E,F represent the hexmer in the asymmetric unit.

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Components

#1: Protein
Hypothetical protein Atu0492


Mass: 17134.537 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: GI:17934405 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 17738839, UniProt: Q7D1C9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M NH4Sulphate, 2% PEG400, 0.1M Hepes Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→65 Å / Num. all: 117258 / Num. obs: 116941 / % possible obs: 99.73 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.74
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.44 / Num. unique all: 8654 / % possible all: 98.88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→64.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.402 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19089 6180 5 %RANDOM
Rwork0.16714 ---
all0.16833 117258 --
obs0.16833 116941 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å20 Å2
2---0.44 Å20 Å2
3---0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.6→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6963 0 0 767 7730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227119
X-RAY DIFFRACTIONr_angle_refined_deg1.121.929648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6045870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06123.451339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.318151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4011554
X-RAY DIFFRACTIONr_chiral_restr0.0750.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025382
X-RAY DIFFRACTIONr_nbd_refined0.2030.23838
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2620
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.238
X-RAY DIFFRACTIONr_mcbond_it0.7161.54454
X-RAY DIFFRACTIONr_mcangle_it1.14227024
X-RAY DIFFRACTIONr_scbond_it2.09133019
X-RAY DIFFRACTIONr_scangle_it3.354.52624
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 411 -
Rwork0.238 8557 -
obs-8654 98.88 %

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