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- PDB-7zr3: STRUCTURE OF ESTER-HYDROLASE EH0 FROM THE METAGENOME OF SORGHUM B... -

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Basic information

Entry
Database: PDB / ID: 7zr3
TitleSTRUCTURE OF ESTER-HYDROLASE EH0 FROM THE METAGENOME OF SORGHUM BICOLOR RHIZOSPHERE FROM THE HENFAES RESEARCH CENTRE (GWYNEDD, WALES)
ComponentsEH0
KeywordsHYDROLASE / ester hydrolase
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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: Appl.Environ.Microbiol. / Year: 2023
Title: The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome.
Authors: Distaso, M. / Cea-Rama, I. / Coscolin, C. / Chernikova, T.N. / Tran, H. / Ferrer, M. / Sanz-Aparicio, J. / Golyshin, P.N.
History
DepositionMay 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 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: EH0
B: EH0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,12510
Polymers73,4972
Non-polymers6288
Water7,782432
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)63.958, 116.666, 128.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPHEPHEAA3 - 1624 - 37
21GLUGLUPHEPHEBB3 - 1624 - 37
12TYRTYRARGARGAA37 - 31758 - 338
22TYRTYRARGARGBB37 - 31758 - 338

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.574761, -0.011867, 0.818236), (-0.005299, -0.99982, -0.018223), (0.818304, -0.01481, 0.574594)4.53399, -23.67794, -6.52646
3given(1), (1), (1)
4given(-0.602634, -0.114632, 0.789742), (-0.05418, -0.981468, -0.183805), (0.796177, -0.153555, 0.585255)6.04181, -20.28413, -5.17277

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EH0


Mass: 36748.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 11% PEG8000, 100mM Bis-Tris pH 5.5, 100mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07218 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2017 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07218 Å / Relative weight: 1
ReflectionResolution: 2.01→64.36 Å / Num. obs: 64849 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Net I/σ(I): 16.6
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4496 / CC1/2: 0.92 / Rpim(I) all: 0.219 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.5.32data scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 2.01→64.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.145 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 3250 5 %RANDOM
Rwork0.1717 ---
obs0.1732 61522 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.58 Å2 / Biso mean: 43.042 Å2 / Biso min: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.38 Å20 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 2.01→64.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 40 433 5214
Biso mean--62.44 48.26 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134942
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174685
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6416740
X-RAY DIFFRACTIONr_angle_other_deg1.3841.57210818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.34521.271236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87815727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2631536
X-RAY DIFFRACTIONr_chiral_restr0.0740.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1240MEDIUM POSITIONAL1.890.5
1240MEDIUM THERMAL10.912
24110MEDIUM POSITIONAL0.390.5
24110MEDIUM THERMAL92
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 220 -
Rwork0.229 4485 -
all-4705 -
obs--100 %

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