[English] 日本語
Yorodumi
- PDB-2ggl: The mutant A222C of Agrobacterium radiobacter N-carbamoyl-D-amino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ggl
TitleThe mutant A222C of Agrobacterium radiobacter N-carbamoyl-D-amino acid amidohydrolase
ComponentsN-carbamoyl-D-amino acid amidohydrolase
KeywordsHYDROLASE / N-Carbamoyl-D-Amino-Acid Amidohydrolase
Function / homology
Function and homology information


N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity
Similarity search - Function
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
N-carbamoyl-D-amino acid hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, W.C. / Chiu, W.C. / You, J.Y.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure-Stability-Activity Relationship in Covalently Cross-linked N-Carbamoyl d-Amino acid Amidohydrolase and N-Acylamino acid Racemase.
Authors: Chiu, W.C. / You, J.Y. / Liu, J.S. / Hsu, S.K. / Hsu, W.H. / Shih, C.H. / Hwang, J.K. / Wang, W.C.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 11, 2006ID: 2FKU
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-carbamoyl-D-amino acid amidohydrolase
B: N-carbamoyl-D-amino acid amidohydrolase
C: N-carbamoyl-D-amino acid amidohydrolase
D: N-carbamoyl-D-amino acid amidohydrolase


Theoretical massNumber of molelcules
Total (without water)136,9654
Polymers136,9654
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: N-carbamoyl-D-amino acid amidohydrolase
D: N-carbamoyl-D-amino acid amidohydrolase


Theoretical massNumber of molelcules
Total (without water)68,4822
Polymers68,4822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-38 kcal/mol
Surface area21140 Å2
MethodPISA
3
A: N-carbamoyl-D-amino acid amidohydrolase
B: N-carbamoyl-D-amino acid amidohydrolase


Theoretical massNumber of molelcules
Total (without water)68,4822
Polymers68,4822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-34 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.379, 68.101, 138.191
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe crystal structure of D-NCAase A222C mutant reveals a tetramer with 222 symmetry.

-
Components

#1: Protein
N-carbamoyl-D-amino acid amidohydrolase


Mass: 34241.129 Da / Num. of mol.: 4 / Mutation: A222C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q44185, N-carbamoyl-D-amino-acid hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 48.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: lithium sulfate, HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 50489 / % possible obs: 94.8 %
Reflection shellResolution: 2.4→2.49 Å / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO6

1fo6


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.977 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20832 2398 5 %RANDOM
Rwork0.16773 ---
all0.169 ---
obs0.16975 45394 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.097 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å2-0.06 Å2
2---0.67 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 0 402 9970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229824
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.94813312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78451204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95923.109476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811576
X-RAY DIFFRACTIONr_chiral_restr0.0910.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027632
X-RAY DIFFRACTIONr_nbd_refined0.2370.34769
X-RAY DIFFRACTIONr_nbtor_refined0.3240.56509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5895
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.59
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 177 -
Rwork0.233 3260 -
obs--93.47 %

+
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://pdbjlvh1.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