[English] 日本語
Yorodumi
- PDB-6eb3: Structural and enzymatic characterization of an esterase from a m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eb3
TitleStructural and enzymatic characterization of an esterase from a metagenomic library
ComponentsEst1
KeywordsHYDROLASE / apha-beta hydrolase / esterase / metagenomic
Function / homologyGAMMA-AMINO-BUTANOIC ACID / 2-hydroxypropane-1,3-diyl dibutanoate / 1,3-dihydroxypropan-2-yl butanoate / PHOSPHATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGuzzo, C.R. / Carvalho, C.F. / Teixeira, R.D. / Farah, C.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/084147 Brazil
Sao Paulo Research Foundation (FAPESP)2013/18664-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)403965/2016-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303677/2017-1 Brazil
CitationJournal: To Be Published
Title: Functional and Structural characterisation of an Esterase from Amazonian Dark Soil
Authors: Guzzo, C.R. / Maciel, N.K. / Barbosa, A.S. / Farah, C.S.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Est1
B: Est1
C: Est1
D: Est1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00620
Polymers117,3724
Non-polymers1,63516
Water7,044391
1
A: Est1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7815
Polymers29,3431
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Est1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7324
Polymers29,3431
Non-polymers3893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Est1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7626
Polymers29,3431
Non-polymers4195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Est1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7305
Polymers29,3431
Non-polymers3874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.650, 105.950, 145.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 268 / Label seq-ID: 1 - 268

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Est1


Mass: 29342.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) metagenome (others)

-
Non-polymers , 8 types, 407 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-J3J / 1,3-dihydroxypropan-2-yl butanoate


Mass: 162.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-J3G / 2-hydroxypropane-1,3-diyl dibutanoate


Mass: 232.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20O5
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 Bis-Tris, pH 6.5, 0.1 M NaCl, 1.3 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 50655 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.77 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.2 / Rpim(I) all: 0.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XUA

2xua


Resolution: 2.35→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.418 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2268 4.9 %RANDOM
Rwork0.19295 ---
obs0.1949 44300 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.35→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8189 0 100 391 8680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198593
X-RAY DIFFRACTIONr_bond_other_d0.0020.028194
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9811666
X-RAY DIFFRACTIONr_angle_other_deg0.983319006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72151085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19123.631358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.867151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2781553
X-RAY DIFFRACTIONr_chiral_restr0.0890.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021683
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6043.514287
X-RAY DIFFRACTIONr_mcbond_other1.6033.514286
X-RAY DIFFRACTIONr_mcangle_it2.6215.2565355
X-RAY DIFFRACTIONr_mcangle_other2.6215.2565356
X-RAY DIFFRACTIONr_scbond_it1.9843.8714306
X-RAY DIFFRACTIONr_scbond_other1.9783.8664303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2875.6676294
X-RAY DIFFRACTIONr_long_range_B_refined5.00241.6039197
X-RAY DIFFRACTIONr_long_range_B_other4.97241.4999142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A162480.1
12B162480.1
21A163960.09
22C163960.09
31A163000.1
32D163000.1
41B163720.09
42C163720.09
51B168420.09
52D168420.09
61C163840.08
62D163840.08
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 167 -
Rwork0.263 3227 -
obs--100 %
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)
10.81090.0848-0.47470.1952-0.49942.224-0.0840.08740.06310.0060.1563-0.0365-0.1254-0.3563-0.07230.0365-0.00210.0140.1076-0.0280.041654.239558.802982.5095
20.0342-0.1099-0.00780.9139-0.84281.71350.0195-0.0271-0.04040.07740.12360.1938-0.14640.026-0.14310.03210.00960.00610.04340.03680.079814.83570.801136.6948
30.6570.15990.22360.07440.13170.83780.04820.00940.0896-0.00850.01960.02250.0397-0.0011-0.06790.0263-0.01250.0080.0090.00640.070825.108190.956499.4285
40.528-0.01310.08130.4104-0.03960.3627-0.05220.010.01780.01410.04650.03330.03080.00750.00570.0354-0.0031-0.00690.016-0.01530.052416.186353.7451101.2803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 268
2X-RAY DIFFRACTION2B1 - 268
3X-RAY DIFFRACTION3C1 - 268
4X-RAY DIFFRACTION4D1 - 268

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more