[English] 日本語
Yorodumi
- PDB-3f4w: The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f4w
TitleThe 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium
ComponentsPutative hexulose 6 phosphate synthase
KeywordsSYNTHASE / LYASE / HUMPS / Malonate / Salmonella typhimurium
Function / homology
Function and homology information


3-hexulose-6-phosphate synthase / hexulose-6-phosphate synthase activity / formaldehyde assimilation via ribulose monophosphate cycle / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / one-carbon metabolic process
Similarity search - Function
3-hexulose-6-phosphate synthase / HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / 3-hexulose-6-phosphate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsVijayalakshmi, J. / Woodard, R.W.
CitationJournal: To be Published
Title: The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium
Authors: Vijayalakshmi, J. / Meredith, T.C. / Woodard, R.W.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative hexulose 6 phosphate synthase
B: Putative hexulose 6 phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6954
Polymers45,4912
Non-polymers2042
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-14 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.971, 108.971, 36.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

-
Components

#1: Protein Putative hexulose 6 phosphate synthase


Mass: 22745.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: STM2755 / Gene: HUMPS, STM2755 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZMP9, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.7M sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MAR CCD 300 / Detector: CCD / Date: Feb 18, 2007 / Details: Si(III) Monochromator
RadiationMonochromator: Si(III) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.65→48.73 Å / Num. obs: 49539 / % possible obs: 94.3 % / Redundancy: 3.21 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.064 / Χ2: 0.81 / Net I/σ(I): 9.6 / Num. measured all: 164432 / Scaling rejects: 5258
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.65-1.712.660.3162.71054236590.6470.7
1.71-1.782.90.33.21501248120.7992.3
1.78-1.8630.2843.51603149990.8596
1.86-1.963.070.2494.11622050450.9196.9
1.96-2.083.150.2084.71630950260.9396.5
2.08-2.243.190.15961643850210.9296.1
2.24-2.463.270.1287.21689050720.8796.5
2.46-2.823.40.0879.61787152120.7998.8
2.82-3.553.670.0515.71945452760.7499.8
3.55-48.733.620.02729.31966554170.799.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREK9.3Ddata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q6O

1q6o


Resolution: 1.65→48.73 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.794 / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.9 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1894 3.82 %RANDOM
Rwork0.213 ---
obs0.214 49530 94.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.869 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 159.54 Å2 / Biso mean: 23.142 Å2 / Biso min: 1.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å2-0 Å20 Å2
2---2.89 Å2-0 Å2
3---5.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 14 500 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043230
X-RAY DIFFRACTIONf_angle_d0.8774370
X-RAY DIFFRACTIONf_chiral_restr0.056534
X-RAY DIFFRACTIONf_plane_restr0.003560
X-RAY DIFFRACTIONf_dihedral_angle_d17.2991202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.6910.418920.3952427251968
1.691-1.7370.3621190.3722960307983
1.737-1.7880.3731380.3363418355697
1.788-1.8460.3381410.323456359796
1.846-1.9120.3141360.2833490362697
1.912-1.9880.3251330.2453451358496
1.988-2.0790.3121360.2243443357996
2.079-2.1880.2681330.2053461359496
2.188-2.3260.2471410.1883447358896
2.326-2.5050.2111360.1963501363797
2.505-2.7570.2821400.1963571371199
2.757-3.1560.2511500.18936253775100
3.156-3.9760.1631470.15236533800100
3.976-48.7550.1741520.1633733388599

+
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