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- PDB-2gz4: 1.5 A Crystal Structure of a Protein of Unknown Function ATU1052 ... -

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Basic information

Entry
Database: PDB / ID: 2gz4
Title1.5 A Crystal Structure of a Protein of Unknown Function ATU1052 from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu1052Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / :
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a hypothetical protein Atu1052 from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Atu1052
B: Hypothetical protein Atu1052
C: Hypothetical protein Atu1052
D: Hypothetical protein Atu1052


Theoretical massNumber of molelcules
Total (without water)91,6264
Polymers91,6264
Non-polymers00
Water22,1401229
1
A: Hypothetical protein Atu1052
C: Hypothetical protein Atu1052


Theoretical massNumber of molelcules
Total (without water)45,8132
Polymers45,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-22 kcal/mol
Surface area16680 Å2
MethodPISA
2
B: Hypothetical protein Atu1052
D: Hypothetical protein Atu1052


Theoretical massNumber of molelcules
Total (without water)45,8132
Polymers45,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-20 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.987, 108.650, 80.955
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is dimer.

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Components

#1: Protein
Hypothetical protein Atu1052 / Hypothesis


Mass: 22906.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: GI:17934959 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UGI5, UniProt: Q7D028*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M NH4 Formate, 12% PEG3350, 4%MPD, pH 7.0, 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: Dec 19, 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: 1.5→80.85 Å / Num. all: 123031 / Num. obs: 119242 / % possible obs: 96.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.07
Reflection shellResolution: 1.5→1.538 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.1 / % possible all: 71.07

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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: 1.5→24.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.393 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18343 6320 5 %RANDOM
Rwork0.15212 ---
obs0.15368 119242 96.92 %-
all-123031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20.11 Å2
2--0 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.031 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6193 0 0 1229 7422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226332
X-RAY DIFFRACTIONr_bond_other_d0.0010.025956
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9618567
X-RAY DIFFRACTIONr_angle_other_deg0.805313745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93621.986287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.059151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5751571
X-RAY DIFFRACTIONr_chiral_restr0.0660.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
X-RAY DIFFRACTIONr_nbd_refined0.2210.21661
X-RAY DIFFRACTIONr_nbd_other0.1870.26348
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23168
X-RAY DIFFRACTIONr_nbtor_other0.0780.23638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1460.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.2139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.55119
X-RAY DIFFRACTIONr_mcbond_other0.2691.51598
X-RAY DIFFRACTIONr_mcangle_it1.28226343
X-RAY DIFFRACTIONr_scbond_it2.0232722
X-RAY DIFFRACTIONr_scangle_it2.7944.52224
X-RAY DIFFRACTIONr_rigid_bond_restr1.199314771
X-RAY DIFFRACTIONr_sphericity_free3.40931229
X-RAY DIFFRACTIONr_sphericity_bonded1.303312149
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 351 -
Rwork0.196 6394 -
obs--71.07 %

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