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- PDB-3zwq: HYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS -

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Basic information

Entry
Database: PDB / ID: 3zwq
TitleHYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS
ComponentsALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN
KeywordsHYDROLASE / HYPERTHERMOPHILIC ENZYME / ESTERASE
Function / homology
Function and homology information


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
Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesPYROBACULUM CALIDIFONTIS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalm, G.J. / Bogdanovic, X. / Hinrichs, W.
Citation
Journal: Appl.Microbiol.Biotechnol. / Year: 2011
Title: The Crystal Structure of an Esterase from 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
DepositionAug 2, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionAug 17, 2011ID: 2WIR
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Dec 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN
B: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)68,7932
Polymers68,7932
Non-polymers00
Water4,432246
1
A: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN
B: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN

A: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN
B: ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)137,5854
Polymers137,5854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area8700 Å2
ΔGint-42.8 kcal/mol
Surface area42410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.919, 127.271, 93.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2134-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95, -0.311, -0.015), (-0.311, 0.95, 0.013), (0.01, 0.017, -1)
Vector: -60.20645, -9.90338, 38.88976)

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Components

#1: Protein ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN / PESTE


Mass: 34396.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM CALIDIFONTIS (archaea) / Strain: VA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: A3MVR4, carboxylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8.5
Details: 2 UL PROTEIN (IN 20 MM TRIS PH 8.0) PLUS 2 UL RESERVOIR (30% MPD, 10% PEG 6000, 0.1 M NAOAC).

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Sep 9, 2008 / Details: OSMIC MULTILAYER
RadiationMonochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. obs: 46646 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 59

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7B

2c7b


Resolution: 2→127 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.594 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2351 5.1 %RANDOM
Rwork0.20509 ---
obs0.20667 43950 91.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---1.13 Å20 Å2
3---2.59 Å2
Refinement stepCycle: LAST / Resolution: 2→127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 0 246 5033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224935
X-RAY DIFFRACTIONr_bond_other_d0.0010.023350
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9696723
X-RAY DIFFRACTIONr_angle_other_deg0.84838129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37522.896221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36415785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7261544
X-RAY DIFFRACTIONr_chiral_restr0.070.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021030
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_it0.4311.53103
X-RAY DIFFRACTIONr_mcbond_other0.1071.51248
X-RAY DIFFRACTIONr_mcangle_it0.76725005
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.24731832
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9614.51715
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 101 -
Rwork0.32 2013 -
obs--57.52 %
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)
117.1499-6.3396-5.168817.33041.798318.9318-0.9204-0.157-0.28091.10460.8545-2.18021.19381.40250.06580.3870.1768-0.31620.2992-0.19750.7324-7.355-9.02819.267
26.88823.2055-1.648913.63660.36820.89770.1863-0.3173-0.0144-0.0252-0.286-0.8932-0.28330.45320.09970.1954-0.2222-0.04760.46140.07140.3975-4.001-7.6520.224
31.7923-0.6201-0.01482.6727-0.74431.4701-0.1060.1457-0.1838-0.17660.1374-0.10140.12860.1143-0.03150.0838-0.01060.03340.1135-0.04560.2475-16.016-27.7280.927
41.64070.51290.25872.08930.39881.3075-0.12540.1360.0501-0.20130.1396-0.1258-0.13830.0732-0.01410.0922-0.020.01850.08540.01260.2484-23.389-12.4691.18
51.67240.01480.34442.33740.15310.9602-0.1508-0.01490.05120.12750.09930.1857-0.03640.03080.05160.09080.02210.0180.0704-0.01030.2157-27.313-14.8549.15
67.4801-4.6513-8.89855.94631.841815.27910.00820.455-0.6538-0.3506-0.41081.02460.5134-0.54710.40250.2704-0.061-0.03680.3011-0.23890.85-51.15-15.72918.74
74.4364-0.0749-0.34015.1081-0.33042.7673-0.0694-0.3504-0.19581.1155-0.08730.48660.5094-0.21760.15670.5951-0.06510.31560.16490.10820.3477-41.755-32.61434.799
82.6857-1.0418-1.48372.03410.53522.7916-0.1751-0.5-0.38770.96260.16820.40170.20.03350.00680.62810.01790.25890.25170.14490.2267-39.024-26.436.632
93.4144-1.11320.93935.47190.4351.7068-0.0141-0.6529-0.34061.29010.2052-0.2680.218-0.0936-0.19110.75690.11840.0460.36950.13650.1157-28.251-24.00339.943
1014.8082-2.3154-2.64238.0557-1.08438.9105-0.3382-0.364-0.51420.639-0.02330.81770.3401-0.60850.36150.23980.00770.15020.1219-0.00610.2917-43.774-5.15927.817
111.356-0.4028-0.44863.33450.89661.3086-0.2006-0.3694-0.10830.96340.15660.1830.1280.03030.04390.45330.08440.09640.22620.06920.1101-31.879-14.73631.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 34
3X-RAY DIFFRACTION3A35 - 147
4X-RAY DIFFRACTION4A148 - 225
5X-RAY DIFFRACTION5A226 - 313
6X-RAY DIFFRACTION6B1 - 24
7X-RAY DIFFRACTION7B25 - 77
8X-RAY DIFFRACTION8B78 - 125
9X-RAY DIFFRACTION9B126 - 196
10X-RAY DIFFRACTION10B197 - 210
11X-RAY DIFFRACTION11B211 - 313

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