[English] 日本語
Yorodumi
- PDB-3giq: Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3giq
TitleCrystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.
ComponentsN-acyl-D-glutamate deacylase
KeywordsHYDROLASE / N-acyl-D-Glutamate Deacylase / amidohydrolase / reaction intermediate
Function / homology
Function and homology information


N-acyl-D-glutamate deacylase / N-acyl-D-glutamate deacylase activity / metal ion binding
Similarity search - Function
D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Dna Ligase; domain 1 ...D-aminoacylase. Domain 3 / D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Dna Ligase; domain 1 / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-[(R)-hydroxy(methyl)phosphoryl]-D-glutamic acid / N-acyl-D-glutamate deacylase / N-acyl-D-glutamate deacylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
Authors: Cummings, J.A. / Fedorov, A.A. / Xu, C. / Brown, S. / Fedorov, E. / Babbitt, P.C. / Almo, S.C. / Raushel, F.M.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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: N-acyl-D-glutamate deacylase
B: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0688
Polymers102,3562
Non-polymers7126
Water11,962664
1
A: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5344
Polymers51,1781
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acyl-D-glutamate deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5344
Polymers51,1781
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.291, 91.291, 507.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein N-acyl-D-glutamate deacylase /


Mass: 51177.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB3285 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7WHC3, UniProt: A0A0H3LXD5*PLUS, N-acyl-D-glutamate deacylase
#2: Chemical ChemComp-G01 / N-[(R)-hydroxy(methyl)phosphoryl]-D-glutamic acid / N-PHOSPHONOMETHYL-D-GLUTAMIC ACID


Type: D-peptide NH3 amino terminus / Mass: 225.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12NO6P
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0M ammonium phosphate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 106991 / Num. obs: 106991 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.065

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GIP

3gip


Resolution: 1.8→24.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2986212 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5336 5 %RANDOM
Rwork0.183 ---
obs0.183 106991 91 %-
all-106991 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.5806 Å2 / ksol: 0.386359 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å21.83 Å20 Å2
2--2.88 Å20 Å2
3----5.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 32 664 7806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.258 359 5 %
Rwork0.243 6865 -
obs-6865 62.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ADG_par.txtADG_top.txt

+
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