[English] 日本語
Yorodumi
- PDB-3m2p: The crystal structure of UDP-N-acetylglucosamine 4-epimerase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m2p
TitleThe crystal structure of UDP-N-acetylglucosamine 4-epimerase from Bacillus cereus
ComponentsUDP-N-acetylglucosamine 4-epimerase
KeywordsISOMERASE / SGXNY / 11155j / UDP / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4-epimerase activity / UDP-N-acetylglucosamine 4-epimerase / nucleotide binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of UDP-N-acetylglucosamine 4-epimerase from Bacillus cereus
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine 4-epimerase
B: UDP-N-acetylglucosamine 4-epimerase
C: UDP-N-acetylglucosamine 4-epimerase
D: UDP-N-acetylglucosamine 4-epimerase
E: UDP-N-acetylglucosamine 4-epimerase
F: UDP-N-acetylglucosamine 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,1427
Polymers211,7376
Non-polymers4041
Water2,054114
1
A: UDP-N-acetylglucosamine 4-epimerase
B: UDP-N-acetylglucosamine 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9833
Polymers70,5792
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-22 kcal/mol
Surface area24010 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine 4-epimerase
F: UDP-N-acetylglucosamine 4-epimerase


Theoretical massNumber of molelcules
Total (without water)70,5792
Polymers70,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-18 kcal/mol
Surface area24220 Å2
MethodPISA
3
D: UDP-N-acetylglucosamine 4-epimerase
E: UDP-N-acetylglucosamine 4-epimerase


Theoretical massNumber of molelcules
Total (without water)70,5792
Polymers70,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.116, 149.725, 166.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details2

-
Components

#1: Protein
UDP-N-acetylglucosamine 4-epimerase


Mass: 35289.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_5271 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Codon+ril Stratagene
References: UniProt: Q814Z6, UDP-N-acetylglucosamine 4-epimerase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.95→111.28 Å / Num. obs: 55533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 64.6 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 13.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 5.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→72.701 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic / σ(F): 1.76 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 2822 5.09 %
Rwork0.2116 --
obs0.2149 55442 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.69 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 49.31 Å2
Baniso -1Baniso -2Baniso -3
1-16.8812 Å2-0 Å2-0 Å2
2---7.5692 Å20 Å2
3----9.312 Å2
Refinement stepCycle: LAST / Resolution: 2.95→72.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 25 114 13067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713198
X-RAY DIFFRACTIONf_angle_d1.05517843
X-RAY DIFFRACTIONf_dihedral_angle_d19.1124667
X-RAY DIFFRACTIONf_chiral_restr0.071983
X-RAY DIFFRACTIONf_plane_restr0.0042302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.00080.31981480.24242593X-RAY DIFFRACTION100
3.0008-3.05540.29471360.24022602X-RAY DIFFRACTION100
3.0554-3.11420.31551610.23162573X-RAY DIFFRACTION100
3.1142-3.17770.27541420.23432588X-RAY DIFFRACTION100
3.1777-3.24680.32181150.23332639X-RAY DIFFRACTION100
3.2468-3.32240.30841430.22662587X-RAY DIFFRACTION100
3.3224-3.40550.27491390.20522591X-RAY DIFFRACTION100
3.4055-3.49750.23411360.18582618X-RAY DIFFRACTION100
3.4975-3.60040.24951380.18232593X-RAY DIFFRACTION100
3.6004-3.71670.25871490.19362624X-RAY DIFFRACTION100
3.7167-3.84950.27381280.19082619X-RAY DIFFRACTION100
3.8495-4.00360.24141490.18482616X-RAY DIFFRACTION100
4.0036-4.18580.24181320.19022621X-RAY DIFFRACTION100
4.1858-4.40640.25411410.18422625X-RAY DIFFRACTION100
4.4064-4.68250.26351320.18582652X-RAY DIFFRACTION100
4.6825-5.04390.26131220.19222654X-RAY DIFFRACTION100
5.0439-5.55140.25281570.1982643X-RAY DIFFRACTION100
5.5514-6.35430.27611500.22862669X-RAY DIFFRACTION100
6.3543-8.00410.26641450.2242701X-RAY DIFFRACTION100
8.0041-72.72320.2711590.23322812X-RAY DIFFRACTION100

+
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