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- PDB-3qyj: Crystal structure of ALR0039, a putative alpha/beta hydrolase fro... -

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Basic information

Entry
Database: PDB / ID: 3qyj
TitleCrystal structure of ALR0039, a putative alpha/beta hydrolase from Nostoc sp PCC 7120.
ComponentsAlr0039 protein
KeywordsHYDROLASE / alpha/beta fold
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
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.778 Å
AuthorsPetit, P. / Kagan, O. / Yakunin, A.F. / Savchenko, A.
CitationJournal: To be Published
Title: Crystal structure of ALR0039, a putative alpha/beta hydrolase from Nostoc sp PCC 7120.
Authors: Petit, P. / Kagan, O. / Yakunin, A.F. / Savchenko, A.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 21, 2015Group: Database references / Structure summary
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr0039 protein
B: Alr0039 protein


Theoretical massNumber of molelcules
Total (without water)66,6782
Polymers66,6782
Non-polymers00
Water11,422634
1
A: Alr0039 protein


Theoretical massNumber of molelcules
Total (without water)33,3391
Polymers33,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alr0039 protein


Theoretical massNumber of molelcules
Total (without water)33,3391
Polymers33,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alr0039 protein

B: Alr0039 protein


Theoretical massNumber of molelcules
Total (without water)66,6782
Polymers66,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area2150 Å2
ΔGint-13 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.542, 88.196, 83.588
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alr0039 protein


Mass: 33339.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / UTEX 2576 / Gene: alr0039 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Z0Q1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 8, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.778→20 Å / Num. all: 61951 / Num. obs: 60343 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 42.8
Reflection shellResolution: 1.778→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.3 / Num. unique all: 5716 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y37

1y37


Resolution: 1.778→19.86 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.854 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17909 2021 3.3 %RANDOM
Rwork0.14852 ---
obs0.14958 58321 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.416 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.16 Å2
2--1.4 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.778→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 634 5328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0214877
X-RAY DIFFRACTIONr_bond_other_d0.0010.023279
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9376643
X-RAY DIFFRACTIONr_angle_other_deg1.10337962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58623.32241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9561531
X-RAY DIFFRACTIONr_chiral_restr0.1390.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021037
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_it1.1371.52923
X-RAY DIFFRACTIONr_mcbond_other0.3731.51164
X-RAY DIFFRACTIONr_mcangle_it1.93224728
X-RAY DIFFRACTIONr_scbond_it3.27131954
X-RAY DIFFRACTIONr_scangle_it4.5934.51909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.778→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.234 4196 -
Rfree-0 -
obs--93.12 %

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