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- PDB-4j07: Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN R... -

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Basic information

Entry
Database: PDB / ID: 4j07
TitleCrystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae
Components6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
KeywordsTRANSFERASE / SSGCID / Mycobacterium leprae / 6 / 7-dimethyl-8-ribityllumazine synthase / DMRL synthase / Lumazine synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
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 speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a Probable Riboflavin Synthase, Beta chain RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,90716
Polymers93,2165
Non-polymers69111
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-53 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.950, 109.950, 288.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase / DMRL synthase / LS / Lumazine synthase


Mass: 18643.135 Da / Num. of mol.: 5 / Fragment: MyleA.00730.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: Br4923 / Gene: MLBr00560, ribH / Plasmid: MyleA.00730.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B8ZUN3, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.71 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MD Morpheus screen C12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM sodium-nitrate, 30mM di-sodium hydrogen phosphate, 30mM ammonium sulfate, 100mM Bicine/Trizma base pH 8.5; MyleA.00730. ...Details: MD Morpheus screen C12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM sodium-nitrate, 30mM di-sodium hydrogen phosphate, 30mM ammonium sulfate, 100mM Bicine/Trizma base pH 8.5; MyleA.00730.a.A1.PS00659 at 20mg/ml; direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 9, 2011
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 76305 / Num. obs: 75991 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Biso Wilson estimate: 27.672 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 19.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-28.150.5234.1627690503696.4
2-2.060.4275.735513499499.2
2.06-2.120.3547.9645376484899
2.12-2.180.28811.29497094726100
2.18-2.250.27612.17479684562100
2.25-2.330.23914.19467554459100
2.33-2.420.20816.06450474264100
2.42-2.520.18117.91434124123100
2.52-2.630.17118.64419073993100
2.63-2.760.14521.9139733381799.9
2.76-2.910.12824.5437541364099.9
2.91-3.080.11926.3635237344799.9
3.08-3.30.10429.6632598325999.9
3.3-3.560.09532.2130170304799.9
3.56-3.90.0933.9927161281499.9
3.9-4.360.08534.9524091257799.9
4.36-5.030.08533.9819430229699.9
5.03-6.170.08930.6916635197599.9
6.17-8.720.07931.612523157299.7
8.72-500.07331.44640195396.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.98 Å
Translation3.5 Å19.98 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W19

1w19


Resolution: 1.95→45.25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.2433 / WRfactor Rwork: 0.2049 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8592 / SU B: 7.375 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1459 / SU Rfree: 0.141 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 3829 5.1 %RANDOM
Rwork0.2081 ---
all0.2101 76305 --
obs0.2101 71727 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.2 Å2 / Biso mean: 22.737 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.05 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 35 467 5856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195571
X-RAY DIFFRACTIONr_bond_other_d0.0010.025542
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9677650
X-RAY DIFFRACTIONr_angle_other_deg0.778312675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5975773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97123.216199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14115869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5541548
X-RAY DIFFRACTIONr_chiral_restr0.0810.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
X-RAY DIFFRACTIONr_mcbond_it0.9391.5143005
X-RAY DIFFRACTIONr_mcbond_other0.9381.5133004
X-RAY DIFFRACTIONr_mcangle_it1.5022.263757
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 280 -
Rwork0.25 5025 -
all-5305 -
obs-4635 96.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67520.076-0.12360.87840.07660.38620.02260.03910.1091-0.03240.03510.0514-0.0524-0.0515-0.05770.04640.0130.02610.02120.04120.092535.70164.71516.222
20.77450.08960.04720.7847-0.05820.3375-0.00990.11880.0349-0.07380.02270.0253-0.02630-0.01280.04580.0080.00990.06930.05530.050948.27352.07-0.989
30.89750.1895-0.26380.6444-0.18990.42120.0212-0.0880.05610.0765-0.0192-0.058-0.00950.0907-0.0020.0355-0.01660.0210.07650.0050.061469.01450.92932.123
40.86290.3504-0.02540.7296-0.23350.4352-0.0007-0.04090.10620.05850.05630.0475-0.07550.0302-0.05560.0345-0.0050.0370.0288-0.01110.079148.58563.76636.306
50.33590.1397-0.22580.5871-0.2120.46310.0143-0.00840.0154-0.0172-0.0015-0.04780.01320.0838-0.01280.03070.00190.01880.08050.04140.055668.40843.8159.087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 159
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1D201 - 202
4X-RAY DIFFRACTION2B12 - 159
5X-RAY DIFFRACTION2A202
6X-RAY DIFFRACTION2B201
7X-RAY DIFFRACTION3C12 - 160
8X-RAY DIFFRACTION3C201
9X-RAY DIFFRACTION3E201
10X-RAY DIFFRACTION4D13 - 158
11X-RAY DIFFRACTION4C202
12X-RAY DIFFRACTION4D203
13X-RAY DIFFRACTION5E13 - 160
14X-RAY DIFFRACTION5B202
15X-RAY DIFFRACTION5E202

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