[English] 日本語
Yorodumi
- PDB-5swu: Dehydroquinate dehydratase from A. fumigatus AroM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5swu
TitleDehydroquinate dehydratase from A. fumigatus AroM
ComponentsPentafunctional AROM polypeptide
KeywordsHYDROLASE / Dehydratase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / 3-dehydroquinate dehydratase, active site / Shikimate kinase, conserved site / Dehydroquinase class I active site. / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / 3-dehydroquinate dehydratase, active site / Shikimate kinase, conserved site / Dehydroquinase class I active site. / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / Shikimate dehydrogenase substrate binding, N-terminal / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 2. / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLight, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Dehydroquinate dehydratase from A. fumigatus AroM
Authors: Light, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pentafunctional AROM polypeptide
B: Pentafunctional AROM polypeptide


Theoretical massNumber of molelcules
Total (without water)58,1182
Polymers58,1182
Non-polymers00
Water4,288238
1
A: Pentafunctional AROM polypeptide


Theoretical massNumber of molelcules
Total (without water)29,0591
Polymers29,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentafunctional AROM polypeptide


Theoretical massNumber of molelcules
Total (without water)29,0591
Polymers29,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.193, 141.397, 46.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Pentafunctional AROM polypeptide


Mass: 29059.248 Da / Num. of mol.: 2 / Fragment: UNP residues 1031-1289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: aroM, AFUB_013230 / Production host: Escherichia coli (E. coli)
References: UniProt: B0XRM8, 3-dehydroquinate synthase, 3-phosphoshikimate 1-carboxyvinyltransferase, shikimate kinase, 3-dehydroquinate dehydratase, shikimate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 48.84 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Protein: 6.1 mg/ml, 0.5 M NaCl, 10 mM Tris pH 8.3, 1 mM BME Crystallization condition: JCSG+ F7 (qiagen), 0.8 M Succinic acid (pH 7)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 31559 / % possible obs: 94.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.812 / % possible all: 72

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.1→28.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.749 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24669 1585 5 %RANDOM
Rwork0.19125 ---
obs0.19398 29930 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.068 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å2-0 Å2-0 Å2
2---2.01 Å20 Å2
3---5.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 0 238 4136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193976
X-RAY DIFFRACTIONr_bond_other_d0.0020.023834
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9655378
X-RAY DIFFRACTIONr_angle_other_deg0.92838818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0523.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6481530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02900
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4023.5422006
X-RAY DIFFRACTIONr_mcbond_other1.4013.5422005
X-RAY DIFFRACTIONr_mcangle_it2.3695.3072504
X-RAY DIFFRACTIONr_mcangle_other2.3695.3082505
X-RAY DIFFRACTIONr_scbond_it1.5513.7561969
X-RAY DIFFRACTIONr_scbond_other1.5513.7571970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6125.5452875
X-RAY DIFFRACTIONr_long_range_B_refined4.96428.4714572
X-RAY DIFFRACTIONr_long_range_B_other4.90128.2014489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 86 -
Rwork0.3 1666 -
obs--72.37 %
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)
11.30920.2768-0.19620.5333-0.28410.66830.01220.0586-0.1108-0.0079-0.0287-0.05910.0009-0.00760.01650.00140.00260.00370.00870.0080.0645-23.738421.9717-15.265
21.48160.01620.0680.71440.10590.62490.0330.15830.14810.07470.01110.1429-0.0806-0.051-0.04420.02470.00760.01740.04940.06360.1209-24.969350.91136.6858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1041 - 1291
2X-RAY DIFFRACTION2B1041 - 1291

+
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