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- PDB-3glv: Crystal structure of the lipopolysaccharide core biosynthesis pro... -

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Basic information

Entry
Database: PDB / ID: 3glv
TitleCrystal structure of the lipopolysaccharide core biosynthesis protein from Thermoplasma volcanium GSS1
ComponentsLipopolysaccharide core biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / lipopolysaccharide core biosynthesis protein / Structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


FMN metabolic process / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / ATP binding
Similarity search - Function
FAD synthase RibL / : / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FAD synthase
Similarity search - Component
Biological speciesThermoplasma volcanium GSS1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsZhang, R. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the lipopolysaccharide core biosynthesis protein from Thermoplasma volcanium GSS1
Authors: Zhang, R. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide core biosynthesis protein
B: Lipopolysaccharide core biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7235
Polymers32,1842
Non-polymers5393
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9.8 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.391, 67.187, 99.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipopolysaccharide core biosynthesis protein


Mass: 16091.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium GSS1 (archaea) / Strain: GSS1 / DSM 4299 / IFO 15438 / JCM 9571 / Gene: GI:14325477, TV1239, TVG1279046 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q979C2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Calcium chloride, 0.1M Tris-HCl, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2008 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 1.99→55.64 Å / Num. all: 27710 / Num. obs: 26291 / % possible obs: 94.88 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 29.67
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2116 / % possible all: 69.61

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.99→55.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.186 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24228 1390 5 %RANDOM
Rwork0.19454 ---
all0.19694 26291 --
obs0.19694 26291 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.994 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2---2.28 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.99→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 33 164 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221971
X-RAY DIFFRACTIONr_bond_other_d0.0010.021347
X-RAY DIFFRACTIONr_angle_refined_deg1.7332.0022653
X-RAY DIFFRACTIONr_angle_other_deg0.95133315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5424.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5291512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it1.0281.51200
X-RAY DIFFRACTIONr_mcbond_other0.2511.5497
X-RAY DIFFRACTIONr_mcangle_it1.89321949
X-RAY DIFFRACTIONr_scbond_it2.9743771
X-RAY DIFFRACTIONr_scangle_it4.6814.5704
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 83 -
Rwork0.292 1390 -
obs-1473 69.61 %
Refinement TLS params.Method: refined / Origin x: 29.011 Å / Origin y: 42.24 Å / Origin z: -9.897 Å
111213212223313233
T0.2604 Å20.0387 Å2-0.023 Å2-0.1421 Å20.0067 Å2--0.0177 Å2
L0.9258 °20.4842 °2-0.8864 °2-1.1041 °2-0.4773 °2--1.5034 °2
S-0.0894 Å °-0.0532 Å °-0.036 Å °-0.0247 Å °-0.0171 Å °-0.0348 Å °0.2213 Å °0.0671 Å °0.1066 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 60
2X-RAY DIFFRACTION1A61 - 121
3X-RAY DIFFRACTION1B0 - 60
4X-RAY DIFFRACTION1B61 - 121

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