[English] 日本語
Yorodumi
- PDB-3hn6: Crystal structure of glucosamine-6-phosphate deaminase from Borre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hn6
TitleCrystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi
ComponentsGlucosamine-6-phosphate deaminase
KeywordsISOMERASE / NIAID / SSGCID / deCODE / UW / SBRI / Infectious Disease / Lyme disease / non-Hodgkin lymphomas / neuroborreliosis / Allosteric enzyme / Carbohydrate metabolism / Hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding / cytosol
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Glucosamine-6-phosphate deaminase from Borrelia burgdorferi
Authors: Edwards, T.E. / Abendroth, J.A. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
E: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6579
Polymers196,1296
Non-polymers5283
Water15,403855
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-61 kcal/mol
Surface area61000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.900, 82.790, 126.990
Angle α, β, γ (deg.)90.000, 109.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 16022 - 181
21METMETLYSLYSBB1 - 16022 - 181
31METMETLYSLYSCC1 - 16022 - 181
41METMETLYSLYSDD1 - 16022 - 181
51METMETLYSLYSEE1 - 16022 - 181
61METMETLYSLYSFF1 - 16022 - 181
12ILEILEASNASNAA190 - 265211 - 286
22ILEILEASNASNBB190 - 265211 - 286
32ILEILEASNASNCC190 - 265211 - 286
42ILEILEASNASNDD190 - 265211 - 286
52ILEILEASNASNEE190 - 265211 - 286
62ILEILEASNASNFF190 - 265211 - 286

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Glucosamine-6-phosphate deaminase / Glucosamine-6-phosphate isomerase / GlcN6P deaminase / GNPDA


Mass: 32688.178 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahis tag followed by 3C protease cleavage site. The tag was not removed prior to crystallization.
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: nagB, BB_0152 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: O30564, glucosamine-6-phosphate deaminase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: JCSG+ sparse matrix screen condition B12, 20% PEG 3350, 0.2 M Potassium phosphate pH 8.3, 27.2 mg/mL protein, 0.1 mg/mL Chymotrypsin, crystal tracking ID 203097b12, VAPOR DIFFUSION, SITTING ...Details: JCSG+ sparse matrix screen condition B12, 20% PEG 3350, 0.2 M Potassium phosphate pH 8.3, 27.2 mg/mL protein, 0.1 mg/mL Chymotrypsin, crystal tracking ID 203097b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 85968 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.993 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.260.2455.6169425606185
2.26-2.320.2735.5216866045194.7
2.32-2.390.2077.1228746011196.2
2.39-2.460.1897.7221195802196.3
2.46-2.540.168.6216305676196.4
2.54-2.630.149.8210175507197
2.63-2.730.12311.4201655336196.7
2.73-2.840.09413.8196145131197.2
2.84-2.970.0815.8188924939197.7
2.97-3.110.06518.8181154744197.7
3.11-3.280.05123173444532198
3.28-3.480.04229.4162264303197.9
3.48-3.720.03734.2149504014198
3.72-4.020.0340.7138473738197.7
4.02-4.40.02445.2132693484198.4
4.4-4.920.02249120733172198.5
4.92-5.680.02246.9105452779198.7
5.68-6.960.02444.590392393198.4
6.96-9.840.0254.468891851198.9
9.84-500.01665.83246905184.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.47 Å
Translation2.5 Å30.47 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NE7

1ne7


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.841 / SU B: 5.646 / SU ML: 0.143 / SU R Cruickshank DPI: 0.293 / SU Rfree: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4330 5 %RANDOM
Rwork0.185 ---
obs0.188 85951 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.46 Å2 / Biso mean: 25.007 Å2 / Biso min: 3.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.19 Å2
2--0.45 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12538 0 27 855 13420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212907
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.93717505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84551628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.425.449602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.448152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8491539
X-RAY DIFFRACTIONr_chiral_restr0.0950.21954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219754
X-RAY DIFFRACTIONr_mcbond_it0.7541.58035
X-RAY DIFFRACTIONr_mcangle_it1.413212987
X-RAY DIFFRACTIONr_scbond_it2.2434872
X-RAY DIFFRACTIONr_scangle_it3.6794.54505
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1217LOOSE POSITIONAL0.315
1B1217LOOSE POSITIONAL0.285
1C1217LOOSE POSITIONAL0.335
1D1217LOOSE POSITIONAL0.235
1E1217LOOSE POSITIONAL0.35
1F1217LOOSE POSITIONAL0.295
1A1217LOOSE THERMAL3.1810
1B1217LOOSE THERMAL2.4510
1C1217LOOSE THERMAL4.7710
1D1217LOOSE THERMAL1.8610
1E1217LOOSE THERMAL310
1F1217LOOSE THERMAL5.5710
2A572LOOSE POSITIONAL0.365
2B572LOOSE POSITIONAL0.275
2C572LOOSE POSITIONAL0.225
2D572LOOSE POSITIONAL0.225
2E572LOOSE POSITIONAL0.295
2F572LOOSE POSITIONAL0.275
2A572LOOSE THERMAL1.8410
2B572LOOSE THERMAL3.5610
2C572LOOSE THERMAL5.1410
2D572LOOSE THERMAL1.610
2E572LOOSE THERMAL2.110
2F572LOOSE THERMAL2.4310
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 270 -
Rwork0.245 5332 -
all-5602 -
obs--85.09 %

+
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