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- PDB-8hfw: The crystal structure of alpha/beta fold hydrolase -

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Basic information

Entry
Database: PDB / ID: 8hfw
TitleThe crystal structure of alpha/beta fold hydrolase
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / Ester synthetase / carboxylesterase / small molecule fatty acid esterase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBurkholderia pyrrocinia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLu, H. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830069 China
CitationJournal: To Be Published
Title: The crystal structure of alpha/beta fold hydrolase
Authors: Lu, H. / Xu, Y.
History
DepositionNov 12, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta fold hydrolase
B: Alpha/beta fold hydrolase
C: Alpha/beta fold hydrolase


Theoretical massNumber of molelcules
Total (without water)97,2083
Polymers97,2083
Non-polymers00
Water5,927329
1
A: Alpha/beta fold hydrolase
B: Alpha/beta fold hydrolase


Theoretical massNumber of molelcules
Total (without water)64,8062
Polymers64,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-17 kcal/mol
Surface area19340 Å2
MethodPISA
2
C: Alpha/beta fold hydrolase

C: Alpha/beta fold hydrolase


Theoretical massNumber of molelcules
Total (without water)64,8062
Polymers64,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2370 Å2
ΔGint-16 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.960, 68.410, 75.340
Angle α, β, γ (deg.)90.000, 93.575, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha/beta fold hydrolase


Mass: 32402.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pyrrocinia (bacteria) / Gene: EVG18_06755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V2WUI0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M Bis-Tris, pH7.2, 0.2 M Magnesium acetate, 17% PEG3350
PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→57.64 Å / Num. obs: 98523 / % possible obs: 98.38 % / Redundancy: 6.37 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.8
Reflection shellResolution: 1.66→1.7 Å / Rmerge(I) obs: 0.466 / Num. unique obs: 98523 / CC1/2: 0.999 / Rrim(I) all: 0.523

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y57
Resolution: 1.66→57.638 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.201 / SU B: 5.215 / SU ML: 0.078 / Average fsc free: 0.9583 / Average fsc work: 0.9733 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2287 4917 4.992 %
Rwork0.1936 93589 -
all0.195 --
obs-98506 98.38 %
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: 27.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.227 Å20 Å20.578 Å2
2---0.983 Å2-0 Å2
3---0.679 Å2
Refinement stepCycle: LAST / Resolution: 1.66→57.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5979 0 0 329 6308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165350
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6438380
X-RAY DIFFRACTIONr_angle_other_deg0.4491.56412361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.461531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8410701
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.47210225
X-RAY DIFFRACTIONr_chiral_restr0.0650.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021226
X-RAY DIFFRACTIONr_nbd_refined0.2290.21407
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24989
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2227
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.26
X-RAY DIFFRACTIONr_nbd_other0.1290.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.227
X-RAY DIFFRACTIONr_mcbond_it2.7321.4673375
X-RAY DIFFRACTIONr_mcbond_other2.7321.4673375
X-RAY DIFFRACTIONr_mcangle_it3.3222.2034206
X-RAY DIFFRACTIONr_mcangle_other3.3222.2034207
X-RAY DIFFRACTIONr_scbond_it3.2681.6242769
X-RAY DIFFRACTIONr_scbond_other3.2681.6242770
X-RAY DIFFRACTIONr_scangle_it3.7532.3634169
X-RAY DIFFRACTIONr_scangle_other3.7532.3634170
X-RAY DIFFRACTIONr_lrange_it4.2629.70426615
X-RAY DIFFRACTIONr_lrange_other4.2529.28126413
X-RAY DIFFRACTIONr_rigid_bond_restr5.374311494
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
1.66-1.7030.2883500.20867240.21274270.9510.97595.24710.182
1.703-1.750.2793490.267180.20471570.9560.97698.74250.171
1.75-1.80.2444030.16965390.17369740.9630.98399.54120.143
1.8-1.8560.243480.1763730.17367540.9630.98399.51140.143
1.856-1.9170.343310.27160450.27566060.910.93996.51830.23
1.917-1.9840.2973070.25957950.26263330.9310.94696.35240.218
1.984-2.0590.232970.17858100.18161380.9680.9899.49490.159
2.059-2.1420.272680.21955310.22159530.9570.96897.41310.195
2.142-2.2380.2182990.18553290.18756600.9710.97999.43460.174
2.238-2.3470.2672340.20649500.20954190.950.96895.66340.189
2.347-2.4730.2222390.17249170.17451650.9670.98299.82580.17
2.473-2.6230.232380.16946540.17248990.9670.98299.85710.173
2.623-2.8040.2162310.18643480.18746090.970.97899.34910.194
2.804-3.0280.2562200.19540550.19842840.9580.97799.78990.209
3.028-3.3160.2471970.20237460.20439550.9640.97699.69660.223
3.316-3.7060.2361480.20233850.20335750.9670.97898.82520.226
3.706-4.2760.1861640.16229880.16332000.980.98498.50.195
4.276-5.230.171440.16225290.16326930.9840.98599.25730.203
5.23-7.3660.202910.22120140.2221080.9820.97399.85770.282
7.366-57.6380.176590.22411390.22112160.9790.96598.51970.307
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1097-0.14550.46691.45670.14491.09530.0167-0.0145-0.06850.04890.03040.0246-0.0106-0.0108-0.04710.00370.0007-0.00040.04450.0030.005232.273-0.353833.0472
21.5548-0.3278-0.98051.36850.28732.75710.15080.254-0.079-0.3838-0.10090.0717-0.1958-0.0201-0.04990.21180.038-0.04930.1507-0.02140.020826.91842.1223.0456
31.63980.1201-0.3321.1887-0.0071.83530.03250.32390.3227-0.2133-0.03150.0505-0.452-0.133-0.0010.18580.0605-0.01850.18170.06290.1855-6.219325.753623.1714
Refinement TLS groupSelection: ALL

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