[English] 日本語
Yorodumi
- PDB-2i3a: Crystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i3a
TitleCrystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase (Rv1652) from Mycobacterium tuberculosis
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / dimer interface beta sandwich / tetramer / Rossmann fold / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / cytoplasm
Similarity search - Function
N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 ...N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / Moraidin, F. / James, M.N.G. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of N-acetyl-gamma-glutamyl-phosphate Reductase from Mycobacterium tuberculosis in Complex with NADP(+).
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Niu, C. / Moradian, F. / James, M.N.G.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2028
Polymers145,3654
Non-polymers8374
Water16,502916
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1014
Polymers72,6822
Non-polymers4182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-14 kcal/mol
Surface area25380 Å2
MethodPISA
2
B: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1014
Polymers72,6822
Non-polymers4182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-13 kcal/mol
Surface area25590 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-73 kcal/mol
Surface area43620 Å2
MethodPISA
4
A: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

B: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2028
Polymers145,3654
Non-polymers8374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area6450 Å2
ΔGint-14 kcal/mol
Surface area52700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.695, 104.031, 138.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 10 - 352 / Label seq-ID: 10 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biologycal assembly is a dimer. There are two dimers in the asymmetric unit.

-
Components

#1: Protein
N-acetyl-gamma-glutamyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 36341.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: argC / Plasmid: pDEST15-1652 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P63562, UniProt: P9WPZ9*PLUS, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG MME 5000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 70645 / Num. obs: 69868 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.23 Å / % possible all: 92.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.412 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 3532 5.1 %RANDOM
Rwork0.16112 ---
obs0.16429 66273 98.62 %-
all-67200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10017 0 56 916 10989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02110293
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.96714094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73251377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23622.299374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.098151419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9551580
X-RAY DIFFRACTIONr_chiral_restr0.1230.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027856
X-RAY DIFFRACTIONr_nbd_refined0.2090.24809
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2860
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.215
X-RAY DIFFRACTIONr_mcbond_it1.0721.56998
X-RAY DIFFRACTIONr_mcangle_it1.726210931
X-RAY DIFFRACTIONr_scbond_it2.74733658
X-RAY DIFFRACTIONr_scangle_it4.3244.53163
Refine LS restraints NCS

Ens-ID: 1 / Number: 2491 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.640.5
2Bmedium positional0.590.5
3Cmedium positional0.510.5
4Dmedium positional0.530.5
1Amedium thermal1.582
2Bmedium thermal1.212
3Cmedium thermal1.232
4Dmedium thermal1.872
LS refinement shellResolution: 2.15→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 256 -
Rwork0.219 4291 -
obs-4291 87.88 %

+
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