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- PDB-2ig8: Crystal structure of a Protein of Unknown Function PA3499 from Ps... -

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Basic information

Entry
Database: PDB / ID: 2ig8
TitleCrystal structure of a Protein of Unknown Function PA3499 from Pseudomonas aeruginosa
ComponentsHypothetical protein PA3499Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein PA3499 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


organonitrogen compound catabolic process / deaminase activity / cytosol
Similarity search - Function
YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 PA3499 from Pseudomonas aeruginosa
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein PA3499
B: Hypothetical protein PA3499
C: Hypothetical protein PA3499


Theoretical massNumber of molelcules
Total (without water)45,8413
Polymers45,8413
Non-polymers00
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-34 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.191, 100.191, 131.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-268-

HOH

21B-149-

HOH

31B-160-

HOH

41B-174-

HOH

51B-255-

HOH

DetailsThis protein exists as trimer. The deposited molecules A, B and C represent the trimer in the asymmetric unit.

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Components

#1: Protein Hypothetical protein PA3499 / Hypothesis


Mass: 15280.443 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3499 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HYB0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl, 3.5M Sodium formate, 4% MPD, pH 7.5, VAPOR DIFFUSION, SITTING 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 7, 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: 1.9→50 Å / Num. obs: 50367 / % possible obs: 99.39 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3868 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.163 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19898 2699 5.1 %RANDOM
Rwork0.17768 ---
all0.17878 50676 --
obs0.17878 50367 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 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: 1.9→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 0 476 3662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223237
X-RAY DIFFRACTIONr_bond_other_d0.0020.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9634401
X-RAY DIFFRACTIONr_angle_other_deg0.93435160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3615424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03723.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40215515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3721527
X-RAY DIFFRACTIONr_chiral_restr0.080.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
X-RAY DIFFRACTIONr_nbd_refined0.2120.2676
X-RAY DIFFRACTIONr_nbd_other0.2010.22355
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21526
X-RAY DIFFRACTIONr_nbtor_other0.0890.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.248
X-RAY DIFFRACTIONr_mcbond_it0.9421.52677
X-RAY DIFFRACTIONr_mcbond_other0.1771.5869
X-RAY DIFFRACTIONr_mcangle_it1.08323347
X-RAY DIFFRACTIONr_scbond_it2.27431260
X-RAY DIFFRACTIONr_scangle_it3.244.51054
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 200 -
Rwork0.242 3494 -
obs-3494 95.5 %
Refinement TLS params.Method: refined / Origin x: 25.517 Å / Origin y: 0.882 Å / Origin z: 0.096 Å
111213212223313233
T-0.1514 Å2-0.0168 Å2-0.0077 Å2-0.2897 Å2-0.0072 Å2---0.1084 Å2
L1.0356 °2-0.2399 °2-0.3884 °2-0.4082 °20.1412 °2--1.9165 °2
S-0.0033 Å °-0.3324 Å °0.0036 Å °0.0019 Å °0.0745 Å °-0.0567 Å °-0.0243 Å °0.7555 Å °-0.0712 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 501 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 142101 - 142
4X-RAY DIFFRACTION1BB1 - 501 - 50
5X-RAY DIFFRACTION1BB51 - 10051 - 100
6X-RAY DIFFRACTION1BB101 - 143101 - 143
7X-RAY DIFFRACTION1CC1 - 501 - 50
8X-RAY DIFFRACTION1CC51 - 10051 - 100
9X-RAY DIFFRACTION1CC101 - 142101 - 142

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