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- PDB-5a62: Hydrolytic potential of the ammonia-oxidizing Thaumarchaeon Nitro... -

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Basic information

Entry
Database: PDB / ID: 5a62
TitleHydrolytic potential of the ammonia-oxidizing Thaumarchaeon Nitrososphaera gargenis - crystal structure and activity profiles of carboxylesterases linked to their metabolic function
ComponentsPUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEINAlpha/beta hydrolase superfamily
KeywordsHYDROLASE
Function / homology
Function and homology information


Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesCandidatus Nitrososphaera gargensis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChow, J. / Kaljunen, H. / Nittinger, E. / Spieck, E. / Rarey, M. / Mueller-Dieckmann, J. / Streit, W.R.
CitationJournal: To be Published
Title: Hydrolytic Potential of the Ammonia-Oxidizing Thaumarchaeon Nitrososphaera Gargenis - Crystal Structure and Activity Profiles of Carboxylesterases Linked to Their Metabolic Function
Authors: Chow, J. / Kaljunen, H. / Nittinger, E. / Spieck, E. / Rarey, M. / Mueller-Dieckmann, J. / Streit, W.R.
History
DepositionJun 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1942
Polymers31,1351
Non-polymers591
Water3,765209
1
A: PUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEIN
hetero molecules

A: PUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3884
Polymers62,2702
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2300 Å2
ΔGint-17.5 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.947, 65.461, 84.591
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-2107-

HOH

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Components

#1: Protein PUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEIN / Alpha/beta hydrolase superfamily


Mass: 31135.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Nitrososphaera gargensis (unknown)
Production host: Escherichia coli BL21(DE3) (unknown) / Variant (production host): ROSETTA-GAMI 2 / References: UniProt: K0IM51
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 44 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M MAGNESIUM ACETATE, 20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2013
RadiationMonochromator: DOUBLE CRYSTAL (SI111, SI311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→51.2 Å / Num. obs: 42828 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 7.3
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 21.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A88
Resolution: 1.5→51.16 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.958 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 274-277 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.16309 2156 5 %RANDOM
Rwork0.14159 ---
obs0.14269 40671 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.07 Å2
2--0.1 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 4 209 2364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192278
X-RAY DIFFRACTIONr_bond_other_d0.0010.022232
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9613092
X-RAY DIFFRACTIONr_angle_other_deg0.91635152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87823.465101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02515419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5311516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6131.4051119
X-RAY DIFFRACTIONr_mcbond_other1.5931.4011117
X-RAY DIFFRACTIONr_mcangle_it2.492.1031405
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7151.7271157
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 151 -
Rwork0.167 3034 -
obs--99.28 %

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