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- PDB-2yh2: Pyrobaculum calidifontis esterase monoclinic form -

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Basic information

Entry
Database: PDB / ID: 2yh2
TitlePyrobaculum calidifontis esterase monoclinic form
ComponentsESTERASE
KeywordsHYDROLASE / HYPERTHERMOPHILIC ENZYME / TERTIARY ALCOHOL / ALPHA/BETA HYDROLASE FOLD
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
Similarity search - Function
Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPYROBACULUM CALIDIFONTIS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPalm, G.J. / Bogdanovic, X. / Hinrichs, W.
Citation
Journal: Appl.Microbiol.Biotechnol. / Year: 2011
Title: The Crystal Structure of an Esterase Fom the Hyperthermophilic Microorganism Pyrobaculum Calidifontis Va1 Supports Explanation of its Enantioselectivity.
Authors: Palm, G.J. / Fernandez-Alvaro, E. / Bogdanovic, X. / Bartsch, S. / Sczodrok, J. / Singh, R.K. / Boettcher, D. / Atomi, H. / Bornscheuer, U.T. / Hinrichs, W.
#1: Journal: Appl.Environ.Microbiol. / Year: 2002
Title: Extremely Stable and Versatile Carboxylesterase from a Hyperthermophilic Archaeon.
Authors: Hotta, Y. / Ezaki, S. / Atomi, H. / Imanaka, T.
History
DepositionApr 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESTERASE
B: ESTERASE
C: ESTERASE
D: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6815
Polymers137,5854
Non-polymers961
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-54 kcal/mol
Surface area42380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.282, 72.335, 141.873
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99979, 0.0018, -0.02032), (0.00748, -0.89429, -0.44742), (-0.01898, -0.44748, 0.89409)29.56792, 56.28368, 13.51402
2given(0.99873, -0.04432, -0.02398), (-0.04407, -0.99897, 0.01071), (-0.02443, -0.00964, -0.99966)2.20997, 42.67968, 71.47411
3given(-0.99955, 0.02984, 0.00103), (0.02727, 0.89815, 0.43885), (0.01217, 0.43868, -0.89856)28.2014, -13.72702, 57.84884
4given(-0.9982, 0.05663, -0.01983), (0.04134, 0.88868, 0.45667), (0.04348, 0.45502, -0.88942)28.74554, -14.69877, 56.58555
5given(0.99941, -0.0336, 0.0065), (-0.03354, -0.99939, -0.00951), (0.00682, 0.00929, -0.99993)0.47794, 43.633, 70.62668
6given(-0.99962, 0.01485, 0.02319), (-0.02367, -0.89352, -0.44839), (0.01406, -0.44877, 0.89354)28.12387, 56.4962, 13.09818

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Components

#1: Protein
ESTERASE / / ALPH-BETA HYDROLASE


Mass: 34396.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM CALIDIFONTIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NKS0, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.14 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8
Details: 10% PEG 4000, 30% MPD, 0.1 M IMIDAZOLE PH 8.0; SOAKED IN 10% PEG 4000, 4% DMSO, 0.1 M IMIDAZOLE PH 8.0, 0.01 M PHENYLBUTANOIC ACID ETHYL ESTER.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97784
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97784 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 50355 / % possible obs: 85 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / % possible all: 47

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLM7.0.4data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIR

2wir
PDB Unreleased entry


Resolution: 2.2→141.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.584 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 2550 5.1 %RANDOM
Rwork0.16416 ---
obs0.16668 47721 84.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.688 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å2-0.32 Å2
2---2.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→141.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9510 0 5 368 9883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229813
X-RAY DIFFRACTIONr_bond_other_d0.0010.026674
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.96713367
X-RAY DIFFRACTIONr_angle_other_deg0.873316179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56622.834441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.996151550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221588
X-RAY DIFFRACTIONr_chiral_restr0.070.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022059
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_it0.4321.56159
X-RAY DIFFRACTIONr_mcbond_other0.0971.52486
X-RAY DIFFRACTIONr_mcangle_it0.8129934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.40233654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.314.53425
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: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 89 -
Rwork0.167 1716 -
obs--41.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.4006-1.0369-0.17619.42391.19322.52640.0232-0.0230.0862-0.70060.2327-0.9512-0.19430.5669-0.25590.1655-0.06180.12840.2383-0.06660.319835.68812.05942.739
20.5083-0.03890.06090.57350.0470.616-0.00010.0173-0.0465-0.0259-0.0148-0.0150.03840.03180.01490.14340.00450.0310.06250.00150.028520.0181.14752.05
31.568-5.3996-0.2619.64984.90034.15020.2370.2551-0.5263-0.8971-0.86272.1343-0.2545-0.64880.62570.13530.01890.01340.38940.03590.4221-7.53127.67745.774
40.43970.0802-0.1130.66850.01980.60340.0121-0.0030.0102-0.0142-0.02130.0218-0.0536-0.02390.00920.14140.0040.03470.0692-0.00770.0268.54132.14859.364
50.54989.26240.155639.43520.59980.94470.35350.0217-0.59051.52380.0273-3.84820.64220.8277-0.38080.47170.2289-0.06110.5972-0.18270.882536.32627.37525.789
60.40720.0512-0.06270.8220.03710.7968-0.00420.01740.0251-0.017-0.0014-0.0328-0.09740.03710.00560.1595-0.00490.04610.06860.00360.023720.89941.30318.904
72.94336.6180.754117.65374.36194.42340.5105-0.38710.35561.1795-0.81781.30650.2499-0.90480.30740.1565-0.01170.10680.39730.06030.2274-7.47116.45524.831
80.517-0.04390.13890.6499-0.02381.22380.05170.0167-0.0211-0.00560.01070.02650.1399-0.0669-0.06240.1437-0.0020.02090.0678-0.00110.0118.26510.59711.731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 27
2X-RAY DIFFRACTION2A28 - 313
3X-RAY DIFFRACTION3B2 - 27
4X-RAY DIFFRACTION4B28 - 313
5X-RAY DIFFRACTION5C2 - 27
6X-RAY DIFFRACTION6C28 - 313
7X-RAY DIFFRACTION7D2 - 27
8X-RAY DIFFRACTION8D28 - 313

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