[English] 日本語
Yorodumi
- PDB-4u8n: Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u8n
TitleStructure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant F66A complexed with UDP
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / NUCLEOTIDE BINDING / MUTASE / FLAVIN ADENINE DINUCLEOTIDE BINDING
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / cell wall organization / nucleotide binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsQureshi, I.A. / Chaudhary, R. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094469 United States
CitationJournal: Biochemistry / Year: 2014
Title: Contributions of Unique Active Site Residues of Eukaryotic UDP-Galactopyranose Mutases to Substrate Recognition and Active Site Dynamics.
Authors: Da Fonseca, I. / Qureshi, I.A. / Mehra-Chaudhary, R. / Kizjakina, K. / Tanner, J.J. / Sobrado, P.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-galactopyranose mutase
B: UDP-galactopyranose mutase
C: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,90836
Polymers228,2104
Non-polymers6,69832
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20580 Å2
ΔGint-192 kcal/mol
Surface area72730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.522, 218.522, 321.114
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-galactopyranose mutase


Mass: 57052.391 Da / Num. of mol.: 4 / Mutation: F66A, K344A, K345A, A429T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: glf, glfA / Production host: Escherichia coli (E. coli) / References: UniProt: Q4W1X2, UDP-galactopyranose mutase

-
Non-polymers , 5 types, 444 molecules

#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.2 - 1.4 M ammonium sulfate and 0.1 M sodium acetate at pH 4.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.3→48.66 Å / Num. obs: 198868 / % possible obs: 99.8 % / Redundancy: 18.1 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.043 / Net I/σ(I): 14.3 / Num. measured all: 3594406 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3416.81.4112.315771793650.710.34796.1
12.58-48.6614.70.04133.72036113890.9990.0198.1

-
Processing

Software
NameVersionClassification
XDS0.1.27data reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UTG

3utg


Resolution: 2.3→48.659 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 9981 5.02 %
Rwork0.1756 188744 -
obs0.1772 198725 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197 Å2 / Biso mean: 44.9446 Å2 / Biso min: 20.78 Å2
Refinement stepCycle: final / Resolution: 2.3→48.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15457 0 421 412 16290
Biso mean--49.73 40.43 -
Num. residues----2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816336
X-RAY DIFFRACTIONf_angle_d1.06922338
X-RAY DIFFRACTIONf_chiral_restr0.0392465
X-RAY DIFFRACTIONf_plane_restr0.0062867
X-RAY DIFFRACTIONf_dihedral_angle_d15.5516005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32370.31353190.2835849616894
2.3237-2.35110.29543360.246862236559100
2.3511-2.37970.28473110.230562536564100
2.3797-2.40990.26283180.223962156533100
2.4099-2.44160.27263240.21962416565100
2.4416-2.4750.26353470.214162166563100
2.475-2.51040.25823410.21562296570100
2.5104-2.54780.25733160.212862536569100
2.5478-2.58770.25693570.209262056562100
2.5877-2.63010.24853080.20162686576100
2.6301-2.67540.23183320.194162466578100
2.6754-2.72410.23953320.195662556587100
2.7241-2.77650.24683210.190662486569100
2.7765-2.83310.2593100.201562806590100
2.8331-2.89470.24773120.208562856597100
2.8947-2.96210.24973180.213362846602100
2.9621-3.03610.26953570.204962546611100
3.0361-3.11820.23523470.210462546601100
3.1182-3.20990.23863180.205963286646100
3.2099-3.31350.23493390.200962616600100
3.3135-3.43190.23053690.200562566625100
3.4319-3.56930.20613350.188563376672100
3.5693-3.73170.21833130.166263226635100
3.7317-3.92830.17913230.15263456668100
3.9283-4.17430.17743340.146763586692100
4.1743-4.49640.153280.12263776705100
4.4964-4.94850.14253480.121163816729100
4.9485-5.66370.16183330.135964526785100
5.6637-7.1320.18323660.160165006866100
7.132-48.67010.17453690.15456769713899
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)
11.3449-0.1049-0.06470.41960.0650.6301-0.02210.43940.0114-0.0628-0.0005-0.0783-0.00520.00120.02440.20080.00570.05690.4170.00190.409572.064177.9437160.747
20.5872-0.29870.00260.7865-0.05660.7328-0.1276-0.1109-0.00350.2790.10560.0742-0.0187-0.00230.02140.34120.07670.01020.2539-0.04360.398124.6351103.4736212.4658
31.4175-0.0438-0.05170.3399-0.05980.8433-0.00290.4905-0.2529-0.09290.02950.00210.10370.0924-0.0230.24-0.0042-0.04680.462-0.12180.404626.098568.6902150.8501
40.6711-0.5532-0.06831.03650.20020.6782-0.1527-0.1653-0.13320.41070.16640.1872-0.0156-0.074-0.01630.43790.10320.05110.2880.09360.426342.704659.994222.9695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resname FDAA0
2X-RAY DIFFRACTION2chain B and not resname FDAB0
3X-RAY DIFFRACTION3chain C and not resname FDAC0
4X-RAY DIFFRACTION4chain D and not resname FDAD0

+
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