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- PDB-3b8x: Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (Col... -

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Basic information

Entry
Database: PDB / ID: 3b8x
TitleCrystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine
ComponentsPyridoxamine 5-phosphate-dependent dehydrase
KeywordsTRANSFERASE / aspartate aminotransferase / colitose / perosamine / o-antigen / PLP / pyridoxal phosphate
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding / metal ion binding
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-G4M / Pyridoxamine 5-phosphate-dependent dehydrase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsCook, P.D. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site.
Authors: Cook, P.D. / Holden, H.M.
History
DepositionNov 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 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)90,66615
Polymers88,6572
Non-polymers2,00913
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.411, 98.123, 119.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 44328.375 Da / Num. of mol.: 2 / Mutation: H188N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O55:H7 / Gene: wbdK / Plasmid: pET28jt / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9F118
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-G4M / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate


Mass: 819.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36N7O19P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 298 K / Method: batch / pH: 6
Details: 28% PEG 3400, 400 mM MgCl2, 100 mM MES, 2 mM 2-oxoglutarate, 10 mM GDP-perosamine, pH 6.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Jul 8, 2007 / Details: montell optics
RadiationMonochromator: ni filter / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 81755 / Num. obs: 75510 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.78 % / Rsym value: 0.085 / Net I/σ(I): 16.24
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.16 / Num. unique all: 9941 / Rsym value: 0.408 / % possible all: 86

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
EPMRphasing
TNTrefinement
PDB_EXTRACT3.004data extraction
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GMU

2gmu


Resolution: 1.7→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 7680 -random
Rwork0.173 ---
all0.177 83883 --
obs0.177 75464 92.4 %-
Displacement parametersBiso mean: 21.268 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 126 665 6989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d17.5

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