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- PDB-3dr7: GDP-perosamine synthase from Caulobacter crescentus with bound GD... -

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Basic information

Entry
Database: PDB / ID: 3dr7
TitleGDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine
ComponentsPutative perosamine synthetase
KeywordsTRANSFERASE / perosamine / pyridoxal phosphate / o-antigen / lipopolysaccharide / aspartate aminotransferase / deoxysugar
Function / homology
Function and homology information


GDP-perosamine synthase / GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity / O antigen biosynthetic process / pyridoxal phosphate 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-GPD / GDP-perosamine synthase / GDP-perosamine synthase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHolden, H.M. / Cook, P.D. / Carney, A.E.
CitationJournal: Biochemistry / Year: 2008
Title: Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase
Authors: Cook, P.D. / Carney, A.E. / Holden, H.M.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3May 17, 2017Group: Source and taxonomy
Revision 1.4Aug 30, 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_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 / _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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative perosamine synthetase
B: Putative perosamine synthetase
C: Putative perosamine synthetase
D: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,48210
Polymers173,0694
Non-polymers2,4146
Water18,7181039
1
A: Putative perosamine synthetase
B: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7415
Polymers86,5342
Non-polymers1,2073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-32.8 kcal/mol
Surface area25400 Å2
MethodPISA
2
C: Putative perosamine synthetase
D: Putative perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7415
Polymers86,5342
Non-polymers1,2073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-27.7 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.414, 152.229, 105.754
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative perosamine synthetase


Mass: 43267.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: Per / Plasmid: pET28T / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: O85354, UniProt: Q9A9H3*PLUS
#2: Chemical
ChemComp-GPD / (2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl


Mass: 572.358 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N6O13P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 50 mM MES, 10% PEG 8000, 1 mM PLP, 1 mM glutamate, pH 6.5, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Apr 28, 2008 / Details: MONTELL
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 161560 / % possible obs: 94.6 % / Redundancy: 3.73 % / Rsym value: 0.086 / Net I/σ(I): 10.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.72 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.424 / % possible all: 83.2

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Processing

Software
NameClassification
cosmodata collection
TNTrefinement
SAINTdata reduction
SADABSdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3BN1

3bn1


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
Rfree0.263 16248 -RANDOM
Rwork0.197 ---
all0.199 170775 --
obs-161554 94.6 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11410 0 156 1039 12605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d16.7
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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