[English] 日本語
Yorodumi
- PDB-4gyn: The E142L mutant of the amidase from Geobacillus pallidus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gyn
TitleThe E142L mutant of the amidase from Geobacillus pallidus
ComponentsAliphatic amidase
KeywordsHYDROLASE / amidase / catalytic tetrad / amidase mechanism
Function / homology
Function and homology information


amidase / indoleacetamide hydrolase activity / amidase activity / :
Similarity search - Function
Aliphatic amidase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWeber, B.W. / Sewell, B.T. / Kimani, S.W. / Varsani, A. / Cowan, D.A. / Hunter, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning.
Authors: Weber, B.W. / Kimani, S.W. / Varsani, A. / Cowan, D.A. / Hunter, R. / Venter, G.A. / Gumbart, J.C. / Sewell, B.T.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aliphatic amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6602
Polymers38,6251
Non-polymers351
Water3,837213
1
A: Aliphatic amidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)231,96212
Polymers231,7496
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation14_445-y-1/2,-x-1/2,-z+1/21
crystal symmetry operation18_445-x-1/2,z-1/2,y+1/21
crystal symmetry operation22_445z-1/2,-y-1/2,x+1/21
Buried area44170 Å2
ΔGint-311 kcal/mol
Surface area51630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.789, 130.789, 130.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-520-

HOH

31A-563-

HOH

41A-585-

HOH

51A-590-

HOH

61A-613-

HOH

71A-660-

HOH

-
Components

#1: Protein Aliphatic amidase / Acylamide amidohydrolase


Mass: 38624.875 Da / Num. of mol.: 1 / Mutation: E142L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: RAPC8 / Gene: amiE, ami / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLysS / References: UniProt: Q9L543, amidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.41 Å3/Da / Density % sol: 49.03 % / Mosaicity: 0.255 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.2M sodium citrate, 0.4M sodium chloride, 0.1M sodium acetate, pH 5.6, vapor diffusion, hanging drop, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: VariMax HF Confocal Optical System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→53.39 Å / Num. obs: 29066 / % possible obs: 94.6 % / Redundancy: 5.66 % / Rmerge(I) obs: 0.205 / Χ2: 1.17 / Net I/σ(I): 5 / Scaling rejects: 1245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.9-1.975.090.5162.31445428241.38693.7
1.97-2.055.840.4732.51647428001.2911493.5
2.05-2.145.850.4143.11657228141.2811693.7
2.14-2.255.90.3633.41683328381.2510193.8
2.25-2.395.890.3293.81690428511.2412294
2.39-2.585.840.2994.21695028821.2212194.8
2.58-2.845.830.2654.71712429221.129195.4
2.84-3.255.80.1996.21711329370.998595.4
3.25-4.095.540.1419.11688530141.0417596.2
4.09-53.395.110.1229.91649131841.0123495.5

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.5Ldata reduction
REFMACrefinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PLQ

2plq


Resolution: 1.9→53.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8555 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1618 / SU Rfree: 0.1434 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1471 5.1 %RANDOM
Rwork0.1942 ---
obs0.1958 29045 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.48 Å2 / Biso mean: 14.5243 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 1 213 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192722
X-RAY DIFFRACTIONr_bond_other_d0.0020.022554
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.9453684
X-RAY DIFFRACTIONr_angle_other_deg0.95135897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49424.597124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76215466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5861513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 101 -
Rwork0.224 1968 -
all-2069 -
obs--93.28 %

+
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