[English] 日本語
Yorodumi
- PDB-3q4g: Structure of NAD synthetase from Vibrio cholerae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q4g
TitleStructure of NAD synthetase from Vibrio cholerae
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha beta / 3-layer(aba) sandwich / Rossmann fold / NAD synthetase
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / NADH metabolic 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
: / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of NAD synthetase from Vibrio cholerae
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,9916
Polymers61,8312
Non-polymers1604
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-85 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.426, 93.426, 165.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 30915.564 Da / Num. of mol.: 2 / Fragment: unp residues 11-285 / Mutation: C37Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: nadE, VCD_000045 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: C3NY23, UniProt: Q9KMW1*PLUS, NAD+ synthase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M sodium formate, 100mM sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 33479 / Num. obs: 33278 / % possible obs: 99.4 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.5 / Redundancy: 13.4 % / Biso Wilson estimate: 33.15 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3117 / % possible all: 95.3

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.7 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.28 / σ(F): 1.44 / σ(I): 2.5 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1668 5.02 %random
Rwork0.1707 ---
all0.1734 33473 --
obs0.1729 33202 99.2 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.751 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 373.96 Å2 / Biso mean: 46.09 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å2-0 Å2-0 Å2
2--6.51 Å20 Å2
3----13.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 4 411 4485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074185
X-RAY DIFFRACTIONf_angle_d0.8475670
X-RAY DIFFRACTIONf_chiral_restr0.061640
X-RAY DIFFRACTIONf_plane_restr0.005746
X-RAY DIFFRACTIONf_dihedral_angle_d12.3611566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.480.3141510.2729073058305893.6
2.48-2.580.2581630.22830783241324198.6
2.58-2.70.261650.20231523317331799.9
2.7-2.840.2411650.18431413306330699.9
2.84-3.020.2331670.18131533320332099.9
3.02-3.250.2151680.17314333113311100
3.25-3.580.2141690.159318433533353100
3.58-4.10.1771700.137318233523352100
4.1-5.160.1921730.133323134043404100
5.16-46.720.2041770.19133633540354099.9
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)
10.74910.58040.53841.52191.01271.6496-0.00040.006-0.0088-0.16740.0126-0.1731-0.13990.2373-0.03270.2065-0.0260.02760.18480.02150.163742.599546.204561.1264
21.9993-1.08752.11032.20110.08593.17260.18060.47570.1118-0.3739-0.25660.5725-0.2265-0.32570.03830.67280.1332-0.03310.3370.00810.257926.312257.789647.9113
30.5832-0.2391-0.36140.76150.50721.93030.11810.16750.1378-0.3251-0.24980.2796-0.5901-0.25040.16620.36560.184-0.0570.18770.03430.15726.068646.704439.9171
40.45210.08680.55050.4940.72441.45650.0230.0024-0.0528-0.2282-0.16550.0822-0.3006-0.15530.10480.21720.04780.01140.20090.00590.194731.848244.801354.3249
50.65080.08790.44592.17351.87931.8960.0403-0.0858-0.2495-0.017-0.53630.4550.1733-0.53940.35150.1637-0.070.01610.3422-0.05860.219324.331131.473860.8079
60.92970.2134-0.26110.89150.29681.25990.0231-0.05240.10550.0787-0.0644-0.00670.1109-0.14140.04350.17790.0387-0.01030.1643-0.00320.19334.019617.303637.7625
70.61880.4484-1.62343.57292.21447.8010.2301-0.0938-0.179-0.7439-0.3922-0.5277-1.3080.2730.23750.48650.1519-0.05690.26790.00150.247935.992334.168220.7945
80.42830.41680.16262.08180.7862.0433-0.05440.21130.1601-0.7936-0.0420.187-0.95210.17160.01520.46850.02560.01370.24510.06070.111936.142142.415730.7213
90.18910.4623-0.0411.55660.44340.70160.09690.05790.0106-0.246-0.028-0.0798-0.34830.0391-0.0580.22860.00740.03040.24110.01320.124940.044928.127234.6715
100.74440.2157-1.22541.73941.70444.5434-0.016-0.2262-0.2991-0.18080.2386-0.3019-0.46580.6787-0.18550.146-0.01650.0080.2864-0.04270.316954.759527.321244.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:78)A1 - 78
2X-RAY DIFFRACTION2(chain A and resid 79:92)A79 - 92
3X-RAY DIFFRACTION3(chain A and resid 93:135)A93 - 135
4X-RAY DIFFRACTION4(chain A and resid 136:214)A136 - 214
5X-RAY DIFFRACTION5(chain A and resid 215:276)A215 - 276
6X-RAY DIFFRACTION6(chain B and resid 1:78)B1 - 78
7X-RAY DIFFRACTION7(chain B and resid 79:92)B79 - 92
8X-RAY DIFFRACTION8(chain B and resid 93:135)B93 - 135
9X-RAY DIFFRACTION9(chain B and resid 136:214)B136 - 214
10X-RAY DIFFRACTION10(chain B and resid 215:276)B215 - 276

+
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