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- PDB-5hha: Structure of PvdO from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5hha
TitleStructure of PvdO from Pseudomonas aeruginosa
ComponentsPvdO
KeywordsHYDROLASE / Chromophore maturation / periplasm
Function / homologypyoverdine biosynthetic process / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / metal ion binding / PvdO
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsBai, G. / Yuan, Z. / Shang, G. / Xia, H. / Gu, L.
CitationJournal: To Be Published
Title: Crystal structure of Chromophore maturation protein from Pseudomonas aeruginosa
Authors: Yuan, Z. / Shang, G. / Bai, G. / Xia, H. / Gu, L.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PvdO
B: PvdO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3304
Polymers63,2502
Non-polymers802
Water16,808933
1
A: PvdO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6652
Polymers31,6251
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PvdO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6652
Polymers31,6251
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.978, 78.924, 58.205
Angle α, β, γ (deg.)90.00, 93.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdO


Mass: 31624.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pvdO, PA2395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I185
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.1M Bis-tris pH5.5, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 137842 / % possible obs: 97.1 % / Redundancy: 3.7 % / Net I/σ(I): 38.75

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.24→37.129 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1652 1950 1.41 %
Rwork0.1505 --
obs0.1507 137842 95.03 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.537 Å2 / ksol: 0.418 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6173 Å2-0 Å20.3147 Å2
2---3.1646 Å20 Å2
3---3.7819 Å2
Refinement stepCycle: LAST / Resolution: 1.24→37.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 2 933 5088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014402
X-RAY DIFFRACTIONf_angle_d1.3265989
X-RAY DIFFRACTIONf_dihedral_angle_d13.0441651
X-RAY DIFFRACTIONf_chiral_restr0.079577
X-RAY DIFFRACTIONf_plane_restr0.009818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2401-1.27110.20391260.19918668X-RAY DIFFRACTION85
1.2711-1.30550.19841290.18279183X-RAY DIFFRACTION91
1.3055-1.34390.21981340.17829349X-RAY DIFFRACTION92
1.3439-1.38730.1741470.16719431X-RAY DIFFRACTION93
1.3873-1.43680.16911290.16459510X-RAY DIFFRACTION94
1.4368-1.49440.18041410.15829672X-RAY DIFFRACTION95
1.4944-1.56240.16121360.15429742X-RAY DIFFRACTION96
1.5624-1.64480.17151390.14629882X-RAY DIFFRACTION97
1.6448-1.74780.15881490.14229927X-RAY DIFFRACTION97
1.7478-1.88280.13231360.13710000X-RAY DIFFRACTION98
1.8828-2.07220.16931480.138210105X-RAY DIFFRACTION99
2.0722-2.3720.15721530.141410115X-RAY DIFFRACTION99
2.372-2.98830.15551370.147510187X-RAY DIFFRACTION99
2.9883-37.14530.16771460.152510121X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 18.2319 Å / Origin y: 10.45 Å / Origin z: -10.4581 Å
111213212223313233
T0.0353 Å20.0026 Å2-0.0136 Å2-0.0284 Å20.0006 Å2--0.0416 Å2
L0.3229 °20.0412 °2-0.1627 °2-0.2145 °20.0076 °2--0.3638 °2
S0.0023 Å °-0.0051 Å °-0.0164 Å °0.0205 Å °-0.0156 Å °-0.0524 Å °-0.0095 Å °0.0012 Å °-0.0441 Å °
Refinement TLS groupSelection details: all

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