[English] 日本語
Yorodumi
- PDB-5kha: Structure of glutamine-dependent NAD+ synthetase from Acinetobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kha
TitleStructure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)
ComponentsGlutamine-dependent NAD+ synthetase
KeywordsLIGASE / SSGCID / Acinetobacter baumannii / Glutamine-dependent NAD+ synthetase / nadE / ADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / NAD+ biosynthetic process / glutaminase activity / ATP binding / cytoplasm
Similarity search - Function
Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase ...Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Structure summary
Revision 1.2Sep 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine-dependent NAD+ synthetase
B: Glutamine-dependent NAD+ synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0598
Polymers123,0092
Non-polymers1,0496
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-87 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 123.750, 73.650
Angle α, β, γ (deg.)90.000, 110.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2:30 or resid 32:33 or (resid...
21(chain B and (resid 2:22 or (resid 23 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASN(chain A and (resid 2:30 or resid 32:33 or (resid...AA2 - 3010 - 38
12ALAALALYSLYS(chain A and (resid 2:30 or resid 32:33 or (resid...AA32 - 3340 - 41
13LYSLYSLYSLYS(chain A and (resid 2:30 or resid 32:33 or (resid...AA3442
14LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
15LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
16LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
17LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
21LYSLYSTHRTHR(chain B and (resid 2:22 or (resid 23 and (name...BB2 - 2210 - 30
22GLNGLNGLNGLN(chain B and (resid 2:22 or (resid 23 and (name...BB2331
23METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
24METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
25METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
26METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029

-
Components

#1: Protein Glutamine-dependent NAD+ synthetase / NAD synthetase / NAD synthetase / Glutamine amidotransferase chain of NAD synthetase / NAD ...NAD synthetase / NAD synthetase / Glutamine amidotransferase chain of NAD synthetase / NAD synthetase/glutamine amidotransferase chain of NAD synthetase / NAD+ synthase / NAD+ synthetase


Mass: 61504.609 Da / Num. of mol.: 2 / Fragment: AcbaC.18002.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: nadE, A7A43_14755, AB895_2341, AB988_2173, ABUW_3069, ACX60_14085, APD31_16600, AQ480_16865, IOMTU433_2979, IX87_01870, TE32_15345
Plasmid: AcbaC.18002.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: V5VHL3, NAD+ synthase (glutamine-hydrolysing), NAD+ synthase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1, condition H5: 20% PEG 3350, 200mM KCl; AcbaC.18002.a.B1.PS02475 at 19.5mg/ml with 2mM of each AMPPNP, Glutamate, MgCl2, PPi; cryo: 20% EG with 2mM NAD/Mg; puck: exo0-1, tray: 266048 h5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 25, 2016 / Details: Rigaku Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 69741 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.542.58198
2.15-2.210.4783.35199.4
2.21-2.280.4293.67198.8
2.28-2.350.3934199.4
2.35-2.420.3284.56199.4
2.42-2.510.3014.76199.7
2.51-2.60.2445.73199.7
2.6-2.710.2186.21199.7
2.71-2.830.1737.14199.6
2.83-2.970.1517.6199.7
2.97-3.130.1169.29199.8
3.13-3.320.08712.421100
3.32-3.550.06418.12199.8
3.55-3.830.05423.7199.5
3.83-4.20.04527.18199
4.2-4.70.03930.9198.9
4.7-5.420.03927.98199.6
5.42-6.640.04622.08199.4
6.64-9.390.03229.89199.5
9.39-500.02344.1195.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å41.24 Å
Translation2.1 Å41.24 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXdev_2429refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f4h

4f4h


Resolution: 2.1→41.242 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 2060 2.96 %RANDOM
Rwork0.165 ---
obs0.1663 69703 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.3 Å2 / Biso mean: 33.9518 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 2.1→41.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8096 0 64 627 8787
Biso mean--33.5 38.05 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078393
X-RAY DIFFRACTIONf_angle_d0.89811414
X-RAY DIFFRACTIONf_chiral_restr0.0551298
X-RAY DIFFRACTIONf_plane_restr0.0051511
X-RAY DIFFRACTIONf_dihedral_angle_d15.2845044
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4741X-RAY DIFFRACTION7.767TORSIONAL
12B4741X-RAY DIFFRACTION7.767TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.31741410.24874399454098
2.1489-2.20260.23321660.215844704636100
2.2026-2.26220.25871340.24483461799
2.2622-2.32870.26111180.19774520463899
2.3287-2.40390.25791470.185444714618100
2.4039-2.48980.27911140.187945324646100
2.4898-2.58950.27041390.17944914630100
2.5895-2.70730.24441340.171845284662100
2.7073-2.850.19721330.169945204653100
2.85-3.02850.23581220.172845414663100
3.0285-3.26220.22171820.166345134695100
3.2622-3.59040.18721290.146545424671100
3.5904-4.10950.14421060.14144550465699
4.1095-5.17590.17141460.12674513465999
5.1759-41.24950.18851490.16464570471999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.59160.1027-0.20810.89790.11971.1950.09370.00340.2637-0.00830.0672-0.2416-0.28640.3312-0.1290.2133-0.07850.02830.2455-0.05950.26131.44535.940656.5893
22.35550.1981-1.13640.96520.00482.0526-0.07430.069-0.3246-0.09480.0789-0.16450.13890.2685-0.00350.151-0.0011-0.02590.1929-0.04990.2293-1.3372-10.539258.661
31.5285-0.8346-0.56720.80220.58471.0233-0.0923-0.3639-0.18760.20450.07560.11530.09680.02610.01310.3269-0.03910.03630.24650.0190.1921-27.3234-3.911588.0476
41.4555-1.13710.531.26-0.53841.64290.0944-0.1432-0.43940.34280.04550.22520.4620.113-0.10790.3299-0.01120.06320.21950.05230.2538-17.9913-14.733283.0363
51.5421.9162-0.36697.3107-0.58251.2299-0.12680.0085-0.04880.01960.0933-0.43410.11670.03390.05070.24830.0115-0.01460.149-0.03240.2634-17.53224.804471.1054
62.8539-1.78330.60511.1278-0.22771.9947-0.03240.02120.13370.05670.0328-0.1195-0.03410.1170.00110.2976-0.00590.02560.1512-0.02550.267-20.271615.588165.163
71.79820.0630.39851.33580.53732.17510.05350.3552-0.199-0.2465-0.1860.2067-0.0234-0.49070.02560.20590.0432-0.02850.3782-0.07180.2153-38.97235.562441.3729
81.4207-0.10530.14291.25380.94551.590.1160.38730.2087-0.4371-0.1450.0391-0.6146-0.29020.04920.39710.134-0.00860.30450.04520.2086-38.587921.864444.7664
91.3501-0.3203-0.07951.241-0.32332.29860.0531-0.29060.26990.4129-0.01580.1146-0.4973-0.2632-0.04620.3350.02660.04390.296-0.06290.2476-46.243619.969481.4772
100.6557-0.2421-0.22411.2784-1.2971.5711-0.0633-0.28070.11090.256-0.0606-0.0677-0.21070.030.14260.3173-0.02970.03370.2384-0.04750.1923-32.500812.401785.1561
111.6494-0.7725-0.20110.925-0.59681.18820.1296-0.11920.52060.3554-0.03920.3517-0.4889-0.2365-0.00630.34590.04470.05060.2338-0.05290.2803-42.084426.707273.778
120.94490.62490.05184.76150.2691.552-0.0210.01390.0302-0.16970.12220.4876-0.026-0.0886-0.04660.1971-0.0239-0.02380.14070.010.2712-34.7458-12.97164.8507
130.0669-0.0001-0.29982.91040.01391.3284-0.005-0.01940.2025-0.04850.04850.181-0.0449-0.2778-0.01860.1797-0.0082-0.01770.2110.0130.2189-28.4161-3.947662.0862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 139 )A2 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 277 )A140 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 421 )A278 - 421
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 466 )A422 - 466
5X-RAY DIFFRACTION5chain 'A' and (resid 467 through 513 )A467 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 541 )A514 - 541
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 139 )B1 - 139
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 277 )B140 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 343 )B278 - 343
10X-RAY DIFFRACTION10chain 'B' and (resid 344 through 421 )B344 - 421
11X-RAY DIFFRACTION11chain 'B' and (resid 422 through 466 )B422 - 466
12X-RAY DIFFRACTION12chain 'B' and (resid 467 through 513 )B467 - 513
13X-RAY DIFFRACTION13chain 'B' and (resid 514 through 541 )B514 - 541

+
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