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- PDB-3lnp: Crystal Structure of Amidohydrolase family Protein OLEI01672_1_46... -

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Basic information

Entry
Database: PDB / ID: 3lnp
TitleCrystal Structure of Amidohydrolase family Protein OLEI01672_1_465 from Oleispira antarctica
ComponentsAmidohydrolase family Protein OLEI01672_1_465
KeywordsHYDROLASE / TIM barrel / beta-fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


S-adenosylhomocysteine deaminase / S-adenosylhomocysteine deaminase activity / S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / metal ion binding
Similarity search - Function
Deaminase MtaD/DadD / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Deaminase MtaD/DadD / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / 5-methylthioadenosine/S-adenosylhomocysteine deaminase
Similarity search - Component
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, Y. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat Commun / Year: 2013
Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Petit, P.A. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidohydrolase family Protein OLEI01672_1_465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9096
Polymers51,6021
Non-polymers3065
Water5,621312
1
A: Amidohydrolase family Protein OLEI01672_1_465
hetero molecules

A: Amidohydrolase family Protein OLEI01672_1_465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,81712
Polymers103,2042
Non-polymers61310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5890 Å2
ΔGint-76 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.902, 77.902, 143.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-550-

HOH

Detailsdimer by operators x,y,z; y,x,-z

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Components

#1: Protein Amidohydrolase family Protein OLEI01672_1_465


Mass: 51602.137 Da / Num. of mol.: 1 / Fragment: OLEI01672_1_465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleispira antarctica (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D3KFX9*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9 % PEG8000, 0.2 M Calcium Acetate, 0.1 M sodium cacodylate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→34.25 Å / Num. all: 30246 / Num. obs: 30246 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 4 / Rsym value: 0.787 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.246 Å / SU ML: 0.22 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1522 5.07 %random
Rwork0.149 ---
all0.151 30032 --
obs0.151 30032 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.832 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--0.5186 Å20 Å20 Å2
2---0.5186 Å2-0 Å2
3---1.0371 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 17 312 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073626
X-RAY DIFFRACTIONf_angle_d1.0564962
X-RAY DIFFRACTIONf_dihedral_angle_d18.5881322
X-RAY DIFFRACTIONf_chiral_restr0.077566
X-RAY DIFFRACTIONf_plane_restr0.004664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1002-2.17520.23181370.18792814295199
2.1752-2.26230.20061460.17122794294099
2.2623-2.36520.19071610.1562810297199
2.3652-2.48990.22191480.15552782293099
2.4899-2.64580.20321590.156328232982100
2.6458-2.850.19891250.15892842296799
2.85-3.13670.19341620.167228573019100
3.1367-3.59010.18691700.152628513021100
3.5901-4.52160.16621540.121629023056100
4.5216-34.25030.15571600.137630353195100
Refinement TLS params.Method: refined / Origin x: -2.1891 Å / Origin y: 27.723 Å / Origin z: 6.8906 Å
111213212223313233
T0.1313 Å20.0148 Å2-0.0119 Å2-0.2528 Å2-0.006 Å2--0.1923 Å2
L0.6647 °2-0.267 °2-0.2718 °2-0.5876 °20.1353 °2--0.5249 °2
S0.067 Å °-0.1186 Å °-0.0146 Å °-0.0296 Å °-0.0706 Å °0.1504 Å °-0.0208 Å °-0.1491 Å °0.0049 Å °
Refinement TLS groupSelection details: chain A

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