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- PDB-5vol: Bacint_04212 ferulic acid esterase -

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Basic information

Entry
Database: PDB / ID: 5vol
TitleBacint_04212 ferulic acid esterase
ComponentsPutative esterase
KeywordsHYDROLASE / ferulic acid esterase / Bacteroides intestinalis / arabinoxylan esterase / carbohydrate esterase family 1 / CE1
Function / homologyEsterase-like / Putative esterase / Alpha/Beta hydrolase fold / ISOPROPYL ALCOHOL / Putative esterase
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKoropatkin, N.M. / Cann, I. / Mackie, R.I.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.
Authors: Wefers, D. / Cavalcante, J.J.V. / Schendel, R.R. / Deveryshetty, J. / Wang, K. / Wawrzak, Z. / Mackie, R.I. / Koropatkin, N.M. / Cann, I.
History
DepositionMay 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative esterase
B: Putative esterase
C: Putative esterase
D: Putative esterase
E: Putative esterase
F: Putative esterase
G: Putative esterase
H: Putative esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,34634
Polymers252,9438
Non-polymers1,40226
Water25,2751403
1
A: Putative esterase
B: Putative esterase
C: Putative esterase
F: Putative esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,29319
Polymers126,4724
Non-polymers82115
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-17 kcal/mol
Surface area39570 Å2
MethodPISA
2
D: Putative esterase
E: Putative esterase
G: Putative esterase
H: Putative esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,05315
Polymers126,4724
Non-polymers58111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-25 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.920, 135.790, 172.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative esterase


Mass: 31617.898 Da / Num. of mol.: 8 / Fragment: UNP residues 21-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_04212 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3CET1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1403 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 10 % v/v 2-propanol, 20 % w/v polyethylene glycol 4000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen vapor
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→56.65 Å / Num. obs: 207704 / % possible obs: 99.63 % / Redundancy: 5.7 % / Biso Wilson estimate: 26.46 Å2 / Rmerge(I) obs: 0.07951 / Net I/σ(I): 16.77
Reflection shellResolution: 1.98→2.051 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7454 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 20663 / CC1/2: 0.757 / % possible all: 99.92

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house SAD model

Resolution: 1.98→56.649 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.1975 10450 5.03 %
Rwork0.1672 --
obs0.1687 207681 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.23 Å2 / Biso mean: 32.6191 Å2 / Biso min: 13.66 Å2
Refinement stepCycle: final / Resolution: 1.98→56.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16996 0 224 1403 18623
Biso mean--54.85 36.06 -
Num. residues----2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717540
X-RAY DIFFRACTIONf_angle_d0.98623720
X-RAY DIFFRACTIONf_chiral_restr0.0422425
X-RAY DIFFRACTIONf_plane_restr0.0053050
X-RAY DIFFRACTIONf_dihedral_angle_d12.6966330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.00250.29863660.265665466912100
2.0025-2.02610.28193690.250265176886100
2.0261-2.05080.2823550.2465076862100
2.0508-2.07670.26993570.240164986855100
2.0767-2.10410.25883480.232865446892100
2.1041-2.13290.2773470.224865286875100
2.1329-2.16340.23633430.210665296872100
2.1634-2.19570.2543550.203165636918100
2.1957-2.230.24853530.206965296882100
2.23-2.26650.25883570.201865376894100
2.2665-2.30560.23523510.197665526903100
2.3056-2.34750.22813860.186664906876100
2.3475-2.39270.22893400.186765876927100
2.3927-2.44150.23243530.187865296882100
2.4415-2.49460.23853110.189766076918100
2.4946-2.55260.23313340.184365826916100
2.5526-2.61650.20533280.179866066934100
2.6165-2.68720.2333420.18365236865100
2.6872-2.76630.2053580.175965606918100
2.7663-2.85560.20933360.169966006936100
2.8556-2.95760.20583640.175165676931100
2.9576-3.0760.20113450.17465396884100
3.076-3.2160.21033290.171466456974100
3.216-3.38560.19213550.1646573692899
3.3856-3.59760.18553220.15226626694899
3.5976-3.87540.16713360.14436622695899
3.8754-4.26520.14723510.1296592694399
4.2652-4.88210.13393090.12166698700799
4.8821-6.14980.16613770.13636635701299
6.1498-56.6720.14533730.13846800717397

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