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- PDB-6vlo: X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoe... -

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Basic information

Entry
Database: PDB / ID: 6vlo
TitleX-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus
ComponentsPutative dTDP-D-glucose 4,6-dehydratase
KeywordsOXIDOREDUCTASE / Acanthamoeba polyphaga minivirus / dehydratase / dideoxysugar / UDP-viosamine
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICKEL (II) ION / THYMIDINE-5'-DIPHOSPHATE / Putative dTDP-D-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsThoden, J.B. / Ferek, J.D. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Biochemical analysis of a sugar 4,6-dehydratase from Acanthamoeba polyphaga Mimivirus.
Authors: Ferek, J.D. / Thoden, J.B. / Holden, H.M.
History
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative dTDP-D-glucose 4,6-dehydratase
B: Putative dTDP-D-glucose 4,6-dehydratase
C: Putative dTDP-D-glucose 4,6-dehydratase
D: Putative dTDP-D-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,06814
Polymers148,6884
Non-polymers4,38010
Water8,791488
1
A: Putative dTDP-D-glucose 4,6-dehydratase
B: Putative dTDP-D-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5347
Polymers74,3442
Non-polymers2,1905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-67 kcal/mol
Surface area24840 Å2
MethodPISA
2
C: Putative dTDP-D-glucose 4,6-dehydratase
D: Putative dTDP-D-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5347
Polymers74,3442
Non-polymers2,1905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-61 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.883, 111.083, 133.385
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
Putative dTDP-D-glucose 4,6-dehydratase


Mass: 37171.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UR12, dTDP-glucose 4,6-dehydratase
#2: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-16% PEG-5000, 2% ethylene glycol, 100 mM HEPES, in the presence of 5 mM dTDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 87647 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 44.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.298 / Num. unique obs: 4281 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R66

1r66


Resolution: 2.05→38.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.43 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.173
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 4517 5.2 %RANDOM
Rwork0.1805 ---
obs0.183 83130 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.3 Å2 / Biso mean: 33.577 Å2 / Biso min: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 2.05→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10133 0 245 488 10866
Biso mean--39.67 38.98 -
Num. residues----1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310647
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179546
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.63614470
X-RAY DIFFRACTIONr_angle_other_deg1.3371.57722154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10151258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.623.235578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.013151784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0211550
X-RAY DIFFRACTIONr_chiral_restr0.0730.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022245
LS refinement shellResolution: 2.05→2.101 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.27 309 -
Rwork0.221 5819 -
obs--94.92 %

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