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- PDB-1x7v: Crystal structure of PA3566 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1x7v
TitleCrystal structure of PA3566 from Pseudomonas aeruginosa
ComponentsPA3566 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / Midwest Center for Structural Genomics / alpha-beta plait / PSI / MCSG
Function / homology
Function and homology information


catalytic activity / oxidoreductase activity / cytosol
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ABM domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsSanders, D.A. / Walker, J.R. / Skarina, T. / Gorodichtchenskaia, E. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2005
Title: The X-ray crystal structure of PA3566 from Pseudomonas aureginosa at 1.8 A resolution.
Authors: Sanders, D.A. / Walker, J.R. / Skarina, T. / Savchenko, A.
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PA3566 protein
B: PA3566 protein
C: PA3566 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5144
Polymers34,4183
Non-polymers961
Water3,531196
1
A: PA3566 protein


Theoretical massNumber of molelcules
Total (without water)11,4731
Polymers11,4731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PA3566 protein


Theoretical massNumber of molelcules
Total (without water)11,4731
Polymers11,4731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PA3566 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,4731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PA3566 protein
B: PA3566 protein
C: PA3566 protein
hetero molecules

A: PA3566 protein
B: PA3566 protein
C: PA3566 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0278
Polymers68,8356
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13520 Å2
ΔGint-49 kcal/mol
Surface area25230 Å2
MethodPISA
5
B: PA3566 protein
C: PA3566 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0413
Polymers22,9452
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-16 kcal/mol
Surface area10520 Å2
MethodPISA
6
A: PA3566 protein

A: PA3566 protein


Theoretical massNumber of molelcules
Total (without water)22,9452
Polymers22,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2380 Å2
ΔGint-3 kcal/mol
Surface area10380 Å2
MethodPISA
7
C: PA3566 protein
hetero molecules

A: PA3566 protein


Theoretical massNumber of molelcules
Total (without water)23,0413
Polymers22,9452
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1000 Å2
ΔGint-21 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.555, 38.395, 63.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PA3566 protein / APC5058


Mass: 11472.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: Q9HY51
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium sulfate, Sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96498, 0.97872, 0.98024
DetectorType: SBC-2 / Detector: CCD / Date: Apr 15, 2004 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964981
20.978721
30.980241
ReflectionResolution: 1.78→50 Å / Num. obs: 25374 / % possible obs: 97.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.8
Reflection shellResolution: 1.78→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.1 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→63.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.152 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.381 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22297 1256 5.1 %RANDOM
Rwork0.1641 ---
obs0.16715 23288 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--1.06 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.78→63.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 5 196 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212428
X-RAY DIFFRACTIONr_bond_other_d0.0010.022179
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9393289
X-RAY DIFFRACTIONr_angle_other_deg0.83235022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9423.066137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.431527
X-RAY DIFFRACTIONr_chiral_restr0.0980.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_nbd_refined0.2140.2430
X-RAY DIFFRACTIONr_nbd_other0.1930.22031
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21102
X-RAY DIFFRACTIONr_nbtor_other0.0860.21517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7651.51795
X-RAY DIFFRACTIONr_mcbond_other0.5511.5591
X-RAY DIFFRACTIONr_mcangle_it2.17422326
X-RAY DIFFRACTIONr_scbond_it3.31731052
X-RAY DIFFRACTIONr_scangle_it4.7284.5963
X-RAY DIFFRACTIONr_rigid_bond_restr1.77135360
X-RAY DIFFRACTIONr_sphericity_free8.6873195
X-RAY DIFFRACTIONr_sphericity_bonded2.77834558
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 69 -
Rwork0.195 1270 -
obs--71.57 %

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