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- PDB-7pp3: STRUCTURE OF ESTER-HYDROLASE EH7 FROM THE METAGENOME OF MARINE SE... -

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Basic information

Entry
Database: PDB / ID: 7pp3
TitleSTRUCTURE OF ESTER-HYDROLASE EH7 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY)
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase
Function / homologyBeta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3-R Spain
CitationJournal: Febs J. / Year: 2022
Title: Crystal structure of a family VIII beta-lactamase fold hydrolase reveals the molecular mechanism for its broad substrate scope.
Authors: Cea-Rama, I. / Coscolin, C. / Gonzalez-Alfonso, J.L. / Raj, J. / Vasiljevic, M. / Plou, F.J. / Ferrer, M. / Sanz-Aparicio, J.
History
DepositionSep 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)192,63817
Polymers191,4694
Non-polymers1,16913
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PISA Analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.937, 102.937, 331.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVALAA9 - 40828 - 427
21ASNASNVALVALBB9 - 40828 - 427
12SERSERASPASPAA8 - 40927 - 428
22SERSERASPASPCC8 - 40927 - 428
13ASNASNVALVALAA9 - 40828 - 427
23ASNASNVALVALDD9 - 40828 - 427
14ASNASNVALVALBB9 - 40828 - 427
24ASNASNVALVALCC9 - 40828 - 427
15ASNASNASPASPBB9 - 40928 - 428
25ASNASNASPASPDD9 - 40928 - 428
16ASNASNVALVALCC9 - 40828 - 427
26ASNASNVALVALDD9 - 40828 - 427

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Esterase


Mass: 47867.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JQ66
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 22% PEG3350, 0.1M Bis-Tris propane 8.5, 0.2M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97898 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.25→49.04 Å / Num. obs: 85057 / % possible obs: 99.5 % / Redundancy: 7 % / CC1/2: 0.988 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.067 / Net I/σ(I): 6.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4503 / CC1/2: 0.775 / Rpim(I) all: 0.276 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.7.1data scaling
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IVK

4ivk


Resolution: 2.25→49.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.398 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4257 5 %RANDOM
Rwork0.1874 ---
obs0.1894 80775 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.07 Å2 / Biso mean: 34.706 Å2 / Biso min: 19.09 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20 Å2
2--3.82 Å20 Å2
3----7.64 Å2
Refinement stepCycle: final / Resolution: 2.25→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12524 0 75 484 13083
Biso mean--59.46 35.78 -
Num. residues----1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312878
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711838
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.64517428
X-RAY DIFFRACTIONr_angle_other_deg1.3661.57327410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63551602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71621.462684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.883152098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561596
X-RAY DIFFRACTIONr_chiral_restr0.0680.21618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022826
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134690.05
12B134690.05
21A134440.06
22C134440.06
31A134890.05
32D134890.05
41B134940.05
42C134940.05
51B135650.04
52D135650.04
61C134330.05
62D134330.05
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 300 -
Rwork0.235 5915 -
all-6215 -
obs--99.49 %

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