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- PDB-7jid: Crystal structure of the L780 UDP-rhamnose synthase from Acantham... -

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Basic information

Entry
Database: PDB / ID: 7jid
TitleCrystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus
ComponentsUDP-L-Rhamnose Synthase
KeywordsOXIDOREDUCTASE / rhamnose / mimivirus
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / S-adenosylmethionine biosynthetic process
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-AWU / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein L780
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBockhaus, N.J. / Ferek, J.D. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
CitationJournal: Protein Sci. / Year: 2020
Title: The high-resolution structure of a UDP-L-rhamnose synthase from Acanthamoeba polyphaga Mimivirus.
Authors: Bockhaus, N.J. / Ferek, J.D. / Thoden, J.B. / Holden, H.M.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-L-Rhamnose Synthase
B: UDP-L-Rhamnose Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,53415
Polymers66,3882
Non-polymers3,14613
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint0 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.803, 52.989, 70.149
Angle α, β, γ (deg.)81.940, 88.680, 66.740
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UDP-L-Rhamnose Synthase / Uncharacterized protein L780


Mass: 33193.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L780 / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: Q5UPS5
#2: Chemical ChemComp-AWU / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 550.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG-8000, 2% DMSO, 100 mM CHES, 5 mM NADP(+), 5 mM UDP-L-rhamnose, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 24, 2019 / Details: helios
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 110458 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rsym value: 0.057 / Net I/σ(I): 13.5
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 18606 / Rsym value: 0.384 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qqr

4qqr


Resolution: 1.45→30.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2058 / WRfactor Rwork: 0.1735 / FOM work R set: 0.7766 / SU B: 1.872 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0767 / SU Rfree: 0.0781 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 5584 5.1 %RANDOM
Rwork0.1978 ---
obs0.1992 104874 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.13 Å2 / Biso mean: 17.528 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.43 Å2-0.18 Å2
2--0.73 Å20.04 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.45→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 181 700 5457
Biso mean--22.24 29.31 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134945
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174531
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.6926705
X-RAY DIFFRACTIONr_angle_other_deg1.4461.59710586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65223.074257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90515888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0181529
X-RAY DIFFRACTIONr_chiral_restr0.1810.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 335 -
Rwork0.387 7049 -
all-7384 -
obs--85.98 %

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