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- PDB-1zl0: Structure of Protein of Unknown Function PA5198 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1zl0
TitleStructure of Protein of Unknown Function PA5198 from Pseudomonas aeruginosa
Componentshypothetical protein PA5198Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PA5198 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / peptidoglycan turnover / peptidoglycan biosynthetic process / serine-type peptidase activity / cell wall organization / regulation of cell shape / proteolysis / cytoplasm
Similarity search - Function
Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 ...Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 / Class I glutamine amidotransferase-like / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Murein tetrapeptide carboxypeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of hypothetical protein PA5198 at 1.1 A resolution.
Authors: Osipiuk, J. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Remark 300 BIOMOLECULE According to authors, the biological assembly for the protein is currently unknown.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA5198
B: hypothetical protein PA5198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,53120
Polymers67,3372
Non-polymers1,19418
Water18,6461035
1
A: hypothetical protein PA5198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2219
Polymers33,6681
Non-polymers5538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein PA5198
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,31011
Polymers33,6681
Non-polymers64210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.678, 79.803, 70.832
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is unknown

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein PA5198 / Hypothesis


Mass: 33668.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5198 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTZ1

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Non-polymers , 7 types, 1053 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M potassium/sodium tartarate, 20% PEG 3350, pH 7.5, temperature 294K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→34.5 Å / Num. all: 233413 / Num. obs: 189940 / % possible obs: 81.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 52.3
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.38 / Num. unique all: 1740 / % possible all: 15

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→34.5 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.602 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12082 4652 2.4 %RANDOM
Rwork0.09866 ---
all0.09921 189926 --
obs0.09921 189926 81.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 74 1035 5760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215260
X-RAY DIFFRACTIONr_bond_other_d0.0020.024964
X-RAY DIFFRACTIONr_angle_refined_deg1.961.977137
X-RAY DIFFRACTIONr_angle_other_deg1.07311510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03322.644261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34915870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141560
X-RAY DIFFRACTIONr_chiral_restr0.1220.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025799
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021081
X-RAY DIFFRACTIONr_nbd_refined0.2780.21242
X-RAY DIFFRACTIONr_nbd_other0.2310.25466
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22515
X-RAY DIFFRACTIONr_nbtor_other0.0930.23096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2809
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2080.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.284
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.711.53149
X-RAY DIFFRACTIONr_mcbond_other0.7461.51283
X-RAY DIFFRACTIONr_mcangle_it2.57625114
X-RAY DIFFRACTIONr_scbond_it3.64332129
X-RAY DIFFRACTIONr_scangle_it5.2454.52023
X-RAY DIFFRACTIONr_rigid_bond_restr1.555310290
X-RAY DIFFRACTIONr_sphericity_free11.27631042
X-RAY DIFFRACTIONr_sphericity_bonded4.3310118
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 66 -
Rwork0.306 2962 -
obs-3028 17.61 %

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