[English] 日本語
Yorodumi
- PDB-4izs: The C145A mutant of the amidase from Nesterenkonia sp. AN1 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4izs
TitleThe C145A mutant of the amidase from Nesterenkonia sp. AN1 in complex with butyramide
ComponentsAmidase
KeywordsHYDROLASE / butyramide
Function / homology
Function and homology information


amidase / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / amidase activity
Similarity search - Function
(R)-stereoselective amidase RamA-like / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BUTYRAMIDE / DI(HYDROXYETHYL)ETHER / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsKimani, S.W. / Sewell, B.T.
CitationJournal: To be Published
Title: Covalent modifications of the active site cysteine occur as a result of mutating the glutamate of the catalytic triad in the amidase from Nesterenkonia sp.
Authors: Kimani, S.W. / Hunter, R. / Vlok, M. / Watermeyer, J. / Sewell, B.T.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4745
Polymers30,0691
Non-polymers4054
Water4,143230
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94810
Polymers60,1372
Non-polymers8118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5400 Å2
ΔGint13 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.320, 114.830, 65.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21A-626-

HOH

31A-630-

HOH

-
Components

#1: Protein Amidase


Mass: 30068.686 Da / Num. of mol.: 1 / Mutation: C145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-BMD / BUTYRAMIDE


Mass: 87.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 2% PEG 400, 2.0 M ammonium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.44→22.951 Å / Num. all: 51279 / Num. obs: 51279 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rsym value: 0.069 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.44-1.5270.38525160473950.38599.8
1.52-1.6170.2642.84895369840.26499.9
1.61-1.7270.1983.64669066270.198100
1.72-1.867.20.1434.74434161790.143100
1.86-2.047.30.0946.84141756800.094100
2.04-2.287.40.0718.73787651530.071100
2.28-2.637.30.0678.83368845860.067100
2.63-3.227.30.0648.82847038880.064100
3.22-4.557.20.03814.82212630540.038100
4.55-22.9516.90.02919.11189317330.02998.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.07 Å
Translation2.5 Å43.07 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKX

3hkx


Resolution: 1.44→22.95 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1793 / WRfactor Rwork: 0.1601 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9061 / SU B: 0.852 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0563 / SU Rfree: 0.0568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 2584 5 %RANDOM
Rwork0.1596 ---
obs0.1606 51256 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.22 Å2 / Biso mean: 15.7782 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.05 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.44→22.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 27 230 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0222094
X-RAY DIFFRACTIONr_angle_refined_deg2.761.9952868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76624.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2611517
X-RAY DIFFRACTIONr_chiral_restr0.2160.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0221650
X-RAY DIFFRACTIONr_mcbond_it1.4911.51338
X-RAY DIFFRACTIONr_mcangle_it2.47422149
X-RAY DIFFRACTIONr_scbond_it3.6783756
X-RAY DIFFRACTIONr_scangle_it6.0434.5706
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 174 -
Rwork0.255 3566 -
all-3740 -
obs--99.65 %

+
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