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- PDB-2r0t: Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with... -

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Basic information

Entry
Database: PDB / ID: 2r0t
TitleCrystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine
ComponentsPyridoxamine 5-phosphate-dependent dehydrase
KeywordsTRANSFERASE / colitose / aspartate aminotransferase / geminal diamine / pyridoxal phosphate
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PGU / Pyridoxamine 5-phosphate-dependent dehydrase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCook, P.D. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2007
Title: A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation
Authors: Cook, P.D. / Holden, H.M.
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct_conn / struct_keywords ...struct_conn / struct_keywords / struct_ref_seq_dif / struct_site
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text ..._struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxamine 5-phosphate-dependent dehydrase
B: Pyridoxamine 5-phosphate-dependent dehydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4434
Polymers88,6872
Non-polymers7572
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.908, 72.905, 86.959
Angle α, β, γ (deg.)90.000, 107.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyridoxamine 5-phosphate-dependent dehydrase / WbdK


Mass: 44343.453 Da / Num. of mol.: 2 / Mutation: H188K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O55:H7 Strain 5a / Gene: wbdK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9F118
#2: Chemical ChemComp-PGU / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLYSINE 188 IS COVALENTLY ATTACHED TO THE PLP-CONTAINING INTERMEDIATE PGU 500

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 298 K / pH: 6
Details: 24% PEG 3400, 100mM MES, 600mM KCl, 2mM PLP, 2mM 2-oxoglutarate, pH 6.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Jun 20, 2007 / Details: montel opics
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 177105 / Num. obs: 60929 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.0626 / Net I/σ(I): 9.87
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.42 % / Mean I/σ(I) obs: 1.55 / Num. unique all: 7757 / Rsym value: 0.4 / % possible all: 83.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
EPMRphasing
TNTrefinement
PDB_EXTRACT3data extraction
cosmodata collection
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GMU

2gmu


Resolution: 1.9→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6003 -random
Rwork0.183 ---
all0.185 65664 --
obs0.185 60923 93 %-
Displacement parametersBiso mean: 40.852 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 0 50 258 6492

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