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- PDB-3bn1: Crystal structure of GDP-perosamine synthase -

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Basic information

Entry
Database: PDB / ID: 3bn1
TitleCrystal structure of GDP-perosamine synthase
ComponentsPerosamine synthetase
KeywordsTRANSFERASE / perosamine / aspartate aminotransferase / deoxysugar / o-antigen
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
ACETATE ION / 2-OXOGLUTARIC ACID / GDP-perosamine synthase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCook, P.D. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2008
Title: GDP-Perosamine Synthase: Structural Analysis and Production of a Novel Trideoxysugar
Authors: Cook, P.D. / Holden, H.M.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Nov 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: Perosamine synthetase
B: Perosamine synthetase
C: Perosamine synthetase
D: Perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,6469
Polymers164,2994
Non-polymers3465
Water18,7721042
1
A: Perosamine synthetase
B: Perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3785
Polymers82,1502
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-32.3 kcal/mol
Surface area25630 Å2
MethodPISA
2
C: Perosamine synthetase
D: Perosamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2684
Polymers82,1502
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-28.4 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.271, 152.933, 105.726
Angle α, β, γ (deg.)90.000, 102.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Perosamine synthetase


Mass: 41074.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Species: Caulobacter vibrioides / Strain: CB15 / Gene: Per / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q9A9H3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: batch / pH: 6.5
Details: 50 mM MES, 10% PEG 8000, 1 mM PLP, 1 mM alpha-ketoglutarate, 50 mM NaCl, pH 6.5, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Nov 16, 2007 / Details: montell optics
RadiationMonochromator: ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 144103 / Num. obs: 141987 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.51 % / Rsym value: 0.08 / Net I/σ(I): 16.86
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 3.44 / Num. unique all: 21555 / Rsym value: 0.36 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
DMphasing
TNTrefinement
PDB_EXTRACT3.004data extraction
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MDO

1mdo


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 14175 -random
Rwork0.176 ---
all0.179 143932 --
obs0.179 141981 98.5 %-
Displacement parametersBiso mean: 22.291 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11320 0 23 1042 12385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_dihedral_angle_d17

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