[English] 日本語
Yorodumi
- PDB-4rdw: The structure of N-formimino-L-Glutamate Iminohydrolase from Pseu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rdw
TitleThe structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-Guanidino-L-Glutaric acid
ComponentsN-formimino-L-Glutamate Iminohydrolase
KeywordsHYDROLASE / AMIDOHYDRALASE FOLD / N-FORMIMINO-L-GLUTAMATE IMINOHYDROLASE / N-Guanidino-L-Glutaric acid
Function / homology
Function and homology information


formimidoylglutamate deiminase / formimidoylglutamate deiminase activity / L-histidine catabolic process / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / deaminase activity / metal ion binding / cytosol
Similarity search - Function
Formiminoglutamate deiminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Formiminoglutamate deiminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-carbamimidoyl-L-glutamic acid / DI(HYDROXYETHYL)ETHER / Formimidoylglutamate deiminase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Marti-Arbona, R. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-Guanidino-L-Glutaric acid
Authors: Fedorov, A.A. / Fedorov, E.V. / Marti-Arbona, R. / Raushel, F.M. / Almo, S.C.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,22710
Polymers49,4041
Non-polymers8239
Water6,702372
1
A: N-formimino-L-Glutamate Iminohydrolase
hetero molecules

A: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,45420
Polymers98,8072
Non-polymers1,64618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area7530 Å2
ΔGint-3 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.223, 133.223, 124.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21A-955-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein N-formimino-L-Glutamate Iminohydrolase


Mass: 49403.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA5106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU77

-
Non-polymers , 6 types, 381 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NGQ / N-carbamimidoyl-L-glutamic acid / N-Guanidino-L-Glutamate


Mass: 189.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M SODIUM MALONATE, 0.1M HEPES, 0.5% JEFFAMINE, pH 7.0, VAPOR DIFFUSION, SITTING 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: Sep 4, 2009
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: 1.591→37.599 Å / Num. obs: 74771 / % possible obs: 99.74 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.591→37.599 Å / SU ML: 0.1 / σ(F): 0 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 2259 3.02 %RANDOM
Rwork0.1493 ---
obs0.1498 74771 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.591→37.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 51 372 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063620
X-RAY DIFFRACTIONf_angle_d1.094904
X-RAY DIFFRACTIONf_dihedral_angle_d13.2071315
X-RAY DIFFRACTIONf_chiral_restr0.078523
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.591-1.62510.18611390.15214420X-RAY DIFFRACTION99
1.6251-1.66290.17071420.14764507X-RAY DIFFRACTION100
1.6629-1.70450.18741320.14564476X-RAY DIFFRACTION100
1.7045-1.75060.16111260.14894501X-RAY DIFFRACTION100
1.7506-1.80210.17351500.14534489X-RAY DIFFRACTION100
1.8021-1.86020.21921200.14314519X-RAY DIFFRACTION100
1.8602-1.92670.16811350.15234507X-RAY DIFFRACTION100
1.9267-2.00390.17381340.14644513X-RAY DIFFRACTION100
2.0039-2.09510.14521240.14764532X-RAY DIFFRACTION100
2.0951-2.20550.17741490.14384491X-RAY DIFFRACTION100
2.2055-2.34370.16861600.14724501X-RAY DIFFRACTION100
2.3437-2.52460.17251420.15044534X-RAY DIFFRACTION100
2.5246-2.77860.16191530.15914532X-RAY DIFFRACTION100
2.7786-3.18050.17651370.15244580X-RAY DIFFRACTION100
3.1805-4.00630.14561570.14424618X-RAY DIFFRACTION100
4.0063-37.610.15911590.15234792X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.3178 Å / Origin y: -15.2102 Å / Origin z: -25.2143 Å
111213212223313233
T0.1418 Å2-0.0097 Å2-0.0038 Å2-0.1547 Å2-0.0232 Å2--0.1296 Å2
L1.0165 °2-0.3001 °2-0.045 °2-0.6818 °2-0.0272 °2--0.3062 °2
S0.0478 Å °0.125 Å °-0.089 Å °-0.1172 Å °-0.038 Å °0.0247 Å °0.0382 Å °-0.0021 Å °-0.0076 Å °
Refinement TLS groupSelection details: chain A

+
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