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- PDB-3gr9: Crystal structure of ColD H188K S187N -

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Basic information

Entry
Database: PDB / ID: 3gr9
TitleCrystal structure of ColD H188K S187N
ComponentsColD
KeywordsTRANSFERASE / colitose / perosamine / PLP / aminotransferase / o-antigen / lipopolysaccharide
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
2-OXOGLUTARIC ACID / Putative pyridoxamine 5-phosphate-dependent dehydrase / Pyridoxamine 5-phosphate-dependent dehydrase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHolden, H.M. / Cook, P.D. / Kubiak, R.L. / Toomey, D.P.
CitationJournal: Biochemistry / Year: 2009
Title: Two Site-Directed Mutations Are Required for the Conversion of a Sugar Dehydratase into an Aminotransferase.
Authors: Cook, P.D. / Kubiak, R.L. / Toomey, D.P. / Holden, H.M.
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 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

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Assembly

Deposited unit
A: ColD
B: ColD
C: ColD
D: ColD
E: ColD
F: ColD
G: ColD
H: ColD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,66514
Polymers356,7898
Non-polymers8776
Water6,539363
1
A: ColD
B: ColD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4894
Polymers89,1972
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-32 kcal/mol
Surface area28170 Å2
MethodPISA
2
C: ColD
D: ColD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4894
Polymers89,1972
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-29 kcal/mol
Surface area28340 Å2
MethodPISA
3
E: ColD
F: ColD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3433
Polymers89,1972
Non-polymers1461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-33 kcal/mol
Surface area28120 Å2
MethodPISA
4
G: ColD
H: ColD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3433
Polymers89,1972
Non-polymers1461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-31 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.728, 114.659, 114.568
Angle α, β, γ (deg.)78.98, 76.23, 76.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ColD / Putative pyridoxamine 5-phosphate-dependent dehydrase (WbdK)


Mass: 44598.598 Da / Num. of mol.: 8 / Mutation: H188K S187N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O55 / Gene: wbdK / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q9F118, UniProt: B1B4V9*PLUS
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 298 K / Method: batch / pH: 6
Details: Precipitant:20-25% PEG 3400, 100 mM MES, 200 mM MgCl2, 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 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 5, 2009 / Details: supper mirrors
RadiationMonochromator: ni / Protocol: 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. all: 168264 / Num. obs: 160879 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Redundancy: 3.42 % / Rsym value: 0.114
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.97 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 19367 / Rsym value: 0.499 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R0T

2r0t


Resolution: 2.2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 15300 -random
Rwork0.177 ---
all0.18 152774 --
obs0.18 152769 90.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24758 0 60 363 25181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONtrigonal planes0.009
X-RAY DIFFRACTIONgeneral planes0.016

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