[English] 日本語
Yorodumi
- PDB-5f23: Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f23
TitleCrystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NH(3)-dependent NAD(+) synthetase / Pseudomonas / NAD / NAD(+) / synthethase / nadE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD+ biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6213
Polymers30,7631
Non-polymers8592
Water4,810267
1
A: NH(3)-dependent NAD(+) synthetase
hetero molecules

A: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2436
Polymers61,5262
Non-polymers1,7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7130 Å2
ΔGint-37 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.870, 41.190, 64.130
Angle α, β, γ (deg.)90.000, 113.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-589-

HOH

31A-662-

HOH

-
Components

#1: Protein NH(3)-dependent NAD(+) synthetase


Mass: 30762.803 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: nadE, PA4920 / Plasmid: PsaeA.00025.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUP3, NAD+ synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen, e1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol; 0.1 M MES/imidazole pH 6.5; PsaeA. ...Details: Morpheus screen, e1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol; 0.1 M MES/imidazole pH 6.5; PsaeA.00025.a.B1.PW37555 at 23.5 mg/ml; 5 h soak with 5mM NAD; cryo: direct; tray 258195e1, puck hml20-1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 20, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 43281 / Num. obs: 42621 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 14.76 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.04 / Χ2: 0.949 / Net I/σ(I): 31.81 / Num. measured all: 432740
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.545.20.9450.3494.4415297320329520.38692.2
1.54-1.580.9370.3325.2617052311829290.36393.9
1.58-1.630.9580.2746.9320973297029120.29498
1.63-1.680.9810.2238.3323360292228720.23898.3
1.68-1.730.990.18110.224025286928370.19298.9
1.73-1.790.9940.14612.3623609271427070.15599.7
1.79-1.860.9960.12214.8924494267926670.12999.6
1.86-1.940.9980.09319.0824522255525510.09899.8
1.94-2.020.9990.07125.3423922240024000.075100
2.02-2.120.9990.05632.9924610237423680.05999.7
2.12-2.240.9990.04939.0223782222722270.052100
2.24-2.370.9990.04344.4523076213621270.04599.6
2.37-2.540.9990.0449.5822225197019620.04299.6
2.54-2.740.9990.03656.4522100188018710.03899.5
2.74-310.03461.9921308170216970.03699.7
3-3.3510.03270.9621146155515500.03399.7
3.35-3.8710.02887.0622289137913770.02999.9
3.87-4.7410.028105.2724452117411710.02999.7
4.74-6.7110.03104.31198469229170.03199.5
6.7110.032104.3106525325270.03399.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_2236)phasing
PHENIX(dev_2236)refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4xfd, apo structure

4xfd


Resolution: 1.5→49.712 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 2066 4.85 %Random selection
Rwork0.1384 40548 --
obs0.1404 42614 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.18 Å2 / Biso mean: 24.9943 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 1.5→49.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 56 271 2309
Biso mean--23.75 33.8 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072181
X-RAY DIFFRACTIONf_angle_d0.8992985
X-RAY DIFFRACTIONf_chiral_restr0.054339
X-RAY DIFFRACTIONf_plane_restr0.006397
X-RAY DIFFRACTIONf_dihedral_angle_d16.5131336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.25251300.17062537X-RAY DIFFRACTION92
1.5349-1.57330.2011240.1572553X-RAY DIFFRACTION94
1.5733-1.61590.19821490.14562633X-RAY DIFFRACTION98
1.6159-1.66340.2021290.13682659X-RAY DIFFRACTION98
1.6634-1.71710.211290.13352696X-RAY DIFFRACTION99
1.7171-1.77850.2051430.12982733X-RAY DIFFRACTION100
1.7785-1.84970.19511420.13282702X-RAY DIFFRACTION100
1.8497-1.93390.25671120.13622772X-RAY DIFFRACTION100
1.9339-2.03590.18621460.12132699X-RAY DIFFRACTION100
2.0359-2.16340.16481610.12622713X-RAY DIFFRACTION100
2.1634-2.33040.18291340.12372729X-RAY DIFFRACTION100
2.3304-2.5650.20441470.13932766X-RAY DIFFRACTION100
2.565-2.93610.19111450.14872733X-RAY DIFFRACTION100
2.9361-3.6990.16561270.14252786X-RAY DIFFRACTION100
3.699-500.14531480.14092837X-RAY DIFFRACTION100

+
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