[English] 日本語
Yorodumi
- PDB-3m83: Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m83
TitleCrystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.12 A resolution (paraoxon inhibitor complex structure)
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / AXE1
Function / homology
Function and homology information


xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / cytoplasm
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2012
Title: Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.
Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / ...Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / Deacon, A.M. / van der Oost, J. / Lesley, S.A. / Elsliger, M.A. / Kengen, S.W. / Wilson, I.A.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Sep 20, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl xylan esterase
B: Acetyl xylan esterase
C: Acetyl xylan esterase
D: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,03729
Polymers232,7946
Non-polymers1,24323
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-168 kcal/mol
Surface area62060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.797, 104.431, 221.644
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
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 3 - 323 / Label seq-ID: 15 - 335

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION FOR THE UNCOMPLEXED PROTEIN.

-
Components

#1: Protein
Acetyl xylan esterase


Mass: 38799.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0077, TM_0077 / Plasmid: MH1 / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WXT2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, Additive: 0.004 M diethyl p-nitrophenyl phosphate (paraoxon), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.12→48.97 Å / Num. obs: 123070 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.92 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.180.5192.2176945355153.5
2.18-2.230.4893.2324466223163.5
2.23-2.30.4563.8380206657170.3
2.3-2.370.3644.9456847325179.2
2.37-2.450.3285.8544578055189.8
2.45-2.530.2937.1676788683199.7
2.53-2.630.2559.17834883651100
2.63-2.740.21410.67574280611100
2.74-2.860.17512.77236977161100
2.86-30.141156927674591100
3-3.160.11517.66521270681100
3.16-3.350.08921.16164667331100
3.35-3.580.074245715663031100
3.58-3.870.0627.6523885882199.9
3.87-4.240.05130.4480265408199.9
4.24-4.740.04632.3440564958199.9
4.74-5.470.0530.4383414369199.9
5.47-6.70.054293224237411100
6.7-9.480.041332536929501100
9.48-48.970.03335.7137991684198.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
PHASERphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: 1vlq

1vlq


Resolution: 2.12→48.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.264 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE PHENYLMETHYLSULFONYL (PMS) MOIETY IS COVALENTLY BOUND TO THE SER 188 IN THE ACTIVE SITE OF A, B, C, D, E AND F CHAINS. 3. THERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE PHENYLMETHYLSULFONYL (PMS) MOIETY IS COVALENTLY BOUND TO THE SER 188 IN THE ACTIVE SITE OF A, B, C, D, E AND F CHAINS. 3. THERE IS AN INCONCLUSIVE PARTIAL ELECTRON DENSITY FOUND IN THE ACTIVE SITE. THIS REMAINED UNMODELED. 3. CALCIUM (CA) AND ACETATE (ACT) IONS FROM CRYSTALLIZATION CONDITIONS, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 6188 5 %RANDOM
Rwork0.168 ---
obs0.169 122994 89.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.72 Å2 / Biso mean: 23.858 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15755 0 68 985 16808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02216532
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211606
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.96122382
X-RAY DIFFRACTIONr_angle_other_deg0.983327966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20151978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65922.905809
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.989152615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.76715122
X-RAY DIFFRACTIONr_chiral_restr0.0860.22264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023749
X-RAY DIFFRACTIONr_nbd_refined0.1980.22924
X-RAY DIFFRACTIONr_nbd_other0.1910.211793
X-RAY DIFFRACTIONr_nbtor_refined0.1810.27735
X-RAY DIFFRACTIONr_nbtor_other0.0860.28102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1840.22
X-RAY DIFFRACTIONr_metal_ion_refined0.080.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.213
X-RAY DIFFRACTIONr_mcbond_it1.775310278
X-RAY DIFFRACTIONr_mcbond_other0.28333956
X-RAY DIFFRACTIONr_mcangle_it2.523515870
X-RAY DIFFRACTIONr_scbond_it4.44687445
X-RAY DIFFRACTIONr_scangle_it5.792116512
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1811TIGHT POSITIONAL0.040.05
2B1811TIGHT POSITIONAL0.040.05
3C1811TIGHT POSITIONAL0.040.05
4D1811TIGHT POSITIONAL0.040.05
5E1811TIGHT POSITIONAL0.040.05
6F1811TIGHT POSITIONAL0.030.05
1A2466MEDIUM POSITIONAL0.220.5
2B2466MEDIUM POSITIONAL0.220.5
3C2466MEDIUM POSITIONAL0.260.5
4D2466MEDIUM POSITIONAL0.230.5
5E2466MEDIUM POSITIONAL0.20.5
6F2466MEDIUM POSITIONAL0.180.5
1A1811TIGHT THERMAL0.190.5
2B1811TIGHT THERMAL0.230.5
3C1811TIGHT THERMAL0.160.5
4D1811TIGHT THERMAL0.170.5
5E1811TIGHT THERMAL0.240.5
6F1811TIGHT THERMAL0.210.5
1A2466MEDIUM THERMAL1.042
2B2466MEDIUM THERMAL1.162
3C2466MEDIUM THERMAL0.942
4D2466MEDIUM THERMAL0.972
5E2466MEDIUM THERMAL1.222
6F2466MEDIUM THERMAL1.12
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 262 -
Rwork0.237 5084 -
all-5346 -
obs--53.48 %

+
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