[English] 日本語
Yorodumi
- PDB-1xyg: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G19940 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xyg
TitleX-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G19940
Componentsputative N-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG / AT2G19940 / CATH 3.40.50 FOLD / SEMIALDEHYDE DEHYDORGENASE FAMILY / TETRAMER
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / chloroplast stroma / chloroplast / NAD binding / protein dimerization activity / copper ion binding / nucleolus
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
Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G19940
Authors: Center for Eukaryotic Structural Genomics
History
DepositionNov 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: 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: putative N-acetyl-gamma-glutamyl-phosphate reductase
B: putative N-acetyl-gamma-glutamyl-phosphate reductase
C: putative N-acetyl-gamma-glutamyl-phosphate reductase
D: putative N-acetyl-gamma-glutamyl-phosphate reductase


Theoretical massNumber of molelcules
Total (without water)158,6024
Polymers158,6024
Non-polymers00
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-81 kcal/mol
Surface area43930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.597, 107.067, 85.754
Angle α, β, γ (deg.)90.00, 118.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
putative N-acetyl-gamma-glutamyl-phosphate reductase /


Mass: 39650.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g19940 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q93Z70
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 MG/ML PROTEIN, 23% PEG2K, 0.200 M TETRAMETHYL AMMONIUM CHLORIDE, 0.100 M MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97167 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2004 / Details: bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97167 Å / Relative weight: 1
ReflectionResolution: 2.19→27.54 Å / Num. obs: 66910 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 24.2 Å2 / Limit h max: 33 / Limit h min: -38 / Limit k max: 47 / Limit k min: -38 / Limit l max: 38 / Limit l min: 0 / Observed criterion F max: 273025.87 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.2-2.253.40.2543.838320.68284.6
2.25-2.310.22640850.6790.4
2.31-2.370.20943360.69595.5
2.37-2.440.19244910.69898.5
2.44-2.520.17445190.73199.8
2.52-2.610.14945620.755100
2.61-2.710.12445360.798100
2.71-2.840.10845610.811100
2.84-2.990.08945430.84100
2.99-3.170.07245570.915100
3.17-3.420.05645560.976100
3.42-3.760.04645381.121100
3.76-4.310.03946041.268100
4.31-5.420.03445821.266100
5.42-500.02846291.02399.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å27.54 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREP8.2.01version5.0:04/07/04phasing
CNS1.1refinement
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VKN

1vkn


Resolution: 2.19→27.54 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.65 / Cross valid method: THROUGHOUT / Details: MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3240 5.1 %random
Rwork0.187 ---
all-68848 --
obs-63968 92.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 61.4749 Å2 / ksol: 0.356645 e/Å3
Displacement parametersBiso max: 126.33 Å2 / Biso mean: 38.85 Å2 / Biso min: 16.29 Å2
Baniso -1Baniso -2Baniso -3
1--7.5 Å20 Å2-1.51 Å2
2--18.99 Å20 Å2
3----11.49 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.19→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10720 0 0 956 11676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.95
X-RAY DIFFRACTIONx_mcbond_it1.491.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it2.242
X-RAY DIFFRACTIONx_scangle_it3.492.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.19-2.290.2823325.30.26159250.0158586625772.9
2.29-2.410.2693855.10.24671080.0148582749387.3
2.41-2.560.2740150.22875630.0148588796492.7
2.56-2.760.2524215.20.2277530.0128580817495.3
2.76-3.040.2464074.90.20679340.0128609834196.9
3.04-3.470.2054164.90.18380260.018595844298.2
3.47-4.370.1794455.20.15681390.0088632858499.4
4.37-27.540.16743350.16482800.0088747871399.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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