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- PDB-1hqk: CRYSTAL STRUCTURE ANALYSIS OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS -

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Basic information

Entry
Database: PDB / ID: 1hqk
TitleCRYSTAL STRUCTURE ANALYSIS OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS
Components6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
KeywordsTRANSFERASE / LUMAZINE SYNTHASE / AQUIFEX AEOLICUS / X-RAY STRUCTURE ANALYSIS / ENZYME STABILITY / VITAMIN BIOSYNTHESIS
Function / homology
Function and homology information


6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Lumazine/riboflavin synthase / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, X. / Meining, W. / Fischer, M. / Bacher, A. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons.
Authors: Zhang, X. / Meining, W. / Fischer, M. / Bacher, A. / Ladenstein, R.
History
DepositionDec 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.6Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)83,6365
Polymers83,6365
Non-polymers00
Water14,412800
1
A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
x 12


Theoretical massNumber of molelcules
Total (without water)1,003,63260
Polymers1,003,63260
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_766-z+2,-x+1,y+11
crystal symmetry operation8_746-z+2,x-1,-y+11
crystal symmetry operation9_645y+1,z-1,x1
crystal symmetry operation10_647-y+1,z-1,-x+21
crystal symmetry operation11_667y+1,-z+1,-x+21
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area250270 Å2
ΔGint-1410 kcal/mol
Surface area250350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)180.820, 180.820, 180.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21D-3341-

HOH

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Components

#1: Protein
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / LUMAZINE SYNTHASE


Mass: 16727.201 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG4000, lithium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.6 mg/mlprotein1drop
250 mMsodium potassium phosphate1droppH7.0
30.5 mMsodium sulfite1drop
40.5 mMEDTA1drop
512 %(w/v)PEG40001reservoir
60.1 Mlithium sulfate1reservoir
70.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 6, 1999
RadiationMonochromator: bent single-crystal germanium triangular monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 1.6→29.33 Å / Num. all: 125160 / Num. obs: 125145 / % possible obs: 97.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.44 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.45
Reflection shellResolution: 1.6→1.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.036 / Num. unique all: 38037
Reflection
*PLUS
Num. measured all: 439597
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.51

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 6302 RANDOM
Rwork0.216 --
all-125160 -
obs-125145 -
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 0 800 6685
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.026
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_dihedral_angle_d23.858
X-RAY DIFFRACTIONx_improper_angle_d1.933
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d

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