[English] 日本語
Yorodumi
- PDB-5nye: A C145A mutant of Nesterenkonia AN1 amidase bound to propionamide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nye
TitleA C145A mutant of Nesterenkonia AN1 amidase bound to propionamide
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / amide / propionamide / cysteine 145 / alanine 145 / nitrilase superfamily
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
DI(HYDROXYETHYL)ETHER / PROPIONAMIDE / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKimani, S.W. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation91532 South Africa
CitationJournal: To be published
Title: Substrate recognition by an amidase of the nitrilase superfamily
Authors: Kimani, S.W. / Venter, G.A. / Sewell, B.T.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4636
Polymers30,0691
Non-polymers3945
Water4,143230
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,92512
Polymers60,1372
Non-polymers78810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5990 Å2
ΔGint-38 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.102, 115.306, 65.348
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-434-

HOH

21A-451-

HOH

31A-562-

HOH

41A-579-

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) / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0VWZ1, amidase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ROP / PROPIONAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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: 2.35 Å3/Da / Density % sol: 47.72 % / Mosaicity: 1.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium, 2% PEG 400, 2.0M Ammonium sulfate

-
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: 1.55→23.63 Å / Num. all: 41219 / Num. obs: 41219 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Rsym value: 0.068 / Net I/av σ(I): 8.4 / Net I/σ(I): 17.1 / Num. measured all: 273901
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.55-1.6360.4211.83573659200.1810.460.4214.498.8
1.63-1.736.20.2852.73450455970.1220.310.2856.299.3
1.73-1.856.30.2023.83337152860.0850.220.2028.699.5
1.85-26.60.1275.93287449630.0520.1380.1271399.7
2-2.196.90.0868.63163345680.0350.0930.08617.999.8
2.19-2.457.10.065112985841800.0260.0710.06522.199.9
2.45-2.837.20.06410.12640736730.0250.0690.06425.799.9
2.83-3.477.20.05810.12256531540.0230.0630.05832.699.9
3.47-4.97.10.03217.31748124720.0130.0350.03242.4100
4.9-24.4536.70.0229.6947214060.0080.0220.0240.299

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.22data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKX

3hkx


Resolution: 1.55→23.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1596 / WRfactor Rwork: 0.1367 / FOM work R set: 0.8956 / SU B: 1.091 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0612 / SU Rfree: 0.0628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 2135 5.1 %RANDOM
Rwork0.1432 ---
obs0.1444 39363 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.88 Å2 / Biso mean: 14.9 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.55→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 25 230 2208
Biso mean--34.05 28.36 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192047
X-RAY DIFFRACTIONr_bond_other_d0.0040.021979
X-RAY DIFFRACTIONr_angle_refined_deg2.4051.9982793
X-RAY DIFFRACTIONr_angle_other_deg1.1683.0014527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29624.06691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791517
X-RAY DIFFRACTIONr_chiral_restr0.1560.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 148 -
Rwork0.206 2876 -
all-3024 -
obs--99.7 %

+
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