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- PDB-9jux: Crystal structure of hyperthermostable carboxylesterase from Anox... -

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Basic information

Entry
Database: PDB / ID: 9jux
TitleCrystal structure of hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9
ComponentsCarboxylesterase
KeywordsHYDROLASE / Carboxylesterase / Anoxybacillus / Thermostable enzyme / Hyper-thermophilic
Function / homologyEsterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Carboxylesterase
Function and homology information
Biological speciesAnoxybacteroides rupiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRahman, N.F.Y.A. / Johan, U.U.M. / Rahman, R.N.Z.R.A. / Noor, N.D.M. / Shariff, F.M. / Ali, M.S.M.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Other government Malaysia
CitationJournal: To Be Published
Title: Crystal structure of carboxylesterase from Bacillus D9
Authors: Rahman, N.F.Y.A. / Johan, U.U.M. / Rahman, R.N.Z.R.A. / Noor, N.D.M. / Shariff, F.M. / Ali, M.S.M.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)83,0093
Polymers83,0093
Non-polymers00
Water3,729207
1
A: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)27,6701
Polymers27,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)27,6701
Polymers27,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)27,6701
Polymers27,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.97, 111.628, 114.885
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxylesterase


Mass: 27669.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacteroides rupiense (bacteria) / Gene: est, GFC29_2339 / Plasmid: pET51b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A160FBT3, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293.15 K / Method: counter-diffusion
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH6.5, 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.667→47.4802 Å / Num. obs: 88855 / % possible obs: 99.58 % / Redundancy: 2 % / Biso Wilson estimate: 26.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.019 / Rpim(I) all: 0.019 / Rrim(I) all: 0.027 / Net I/σ(I): 16.2
Reflection shellResolution: 1.67→47.48 Å / Num. unique obs: 88855 / CC1/2: 0.999 / % possible all: 99.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSdata reduction
Coot0.9.8.95model building
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→47.48 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.842 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.103 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2253 4453 5.036 %
Rwork0.1679 83976 -
all0.171 --
obs-88429 99.723 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.096 Å2-0 Å20 Å2
2---2.162 Å20 Å2
3---2.258 Å2
Refinement stepCycle: LAST / Resolution: 1.67→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 0 207 6048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125991
X-RAY DIFFRACTIONr_angle_refined_deg2.2521.8428109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.557527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.025101053
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.26510279
X-RAY DIFFRACTIONr_chiral_restr0.1440.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024593
X-RAY DIFFRACTIONr_nbd_refined0.2110.22678
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.214
X-RAY DIFFRACTIONr_mcbond_it5.5851.7432901
X-RAY DIFFRACTIONr_mcangle_it7.4363.1363621
X-RAY DIFFRACTIONr_scbond_it8.4312.0643090
X-RAY DIFFRACTIONr_scangle_it11.2613.6654488
X-RAY DIFFRACTIONr_lrange_it13.01320.0929056
X-RAY DIFFRACTIONr_rigid_bond_restr7.48235991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.67-1.7130.3263340.30859950.30964630.9220.9597.92670.294
1.713-1.760.3093380.24658750.24963070.9550.97398.50960.222
1.76-1.8110.263260.20757950.20961220.9580.98199.98370.175
1.811-1.8670.2663080.16656670.17159750.9580.9861000.132
1.867-1.9280.2193000.15855040.16158040.9720.9871000.125
1.928-1.9950.2142470.1553460.15355930.970.9881000.122
1.995-2.0710.2042750.14951500.15254270.970.98899.96320.125
2.071-2.1550.2322520.15149460.15551980.9670.9881000.128
2.155-2.2510.2092640.1547670.15450310.9720.9871000.132
2.251-2.360.2462280.15145860.15648140.9590.9871000.137
2.36-2.4880.2481850.16643820.16945670.9620.9841000.153
2.488-2.6380.2672490.16940780.17443270.9570.9831000.162
2.638-2.820.2432320.18638690.18941010.960.9781000.185
2.82-3.0450.2342100.18535860.18737970.9640.97999.97370.188
3.045-3.3340.2081550.17933750.1835310.9730.9899.97170.19
3.334-3.7250.2161320.1630900.16232220.9740.9861000.178
3.725-4.2970.2011630.14726770.1528400.9780.9881000.171
4.297-5.2520.1851260.14323180.14524440.9850.9891000.173
5.252-7.3820.276860.20918440.21219340.9670.97999.79320.249
7.382-47.480.162410.16311080.16311500.9860.98599.9130.211
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)
11.669-0.2997-0.00731.44390.2371.2801-0.0596-0.03240.09870.02520.00520.12130.001-0.13390.05440.0552-0.0238-0.00780.1137-0.00380.02112.690911.653427.8688
21.66680.18360.00651.4251-0.2031.44380.01580.0414-0.0839-0.0426-0.0182-0.10660.04380.07150.00240.04640.0003-0.00240.0992-0.00210.01157.1676-15.101153.1542
31.82430.07350.28371.59790.08381.19820.0076-0.02330.1548-0.0512-0.0301-0.1309-0.03010.06220.02250.06650.00190.03260.1231-0.01660.0601-10.956713.920468.5912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA5 - 246
2X-RAY DIFFRACTION2ALLB5 - 246
3X-RAY DIFFRACTION3ALLC5 - 246

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