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- PDB-5a88: Crystal structure of the riboflavin kinase module of FAD syntheta... -

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Basic information

Entry
Database: PDB / ID: 5a88
TitleCrystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with ADP
ComponentsRIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
KeywordsTRANSFERASE / RIBOFLAVIN KINASE DOMAIN / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


riboflavin kinase / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / ATP binding
Similarity search - Function
Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 ...Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Bifunctional riboflavin kinase/FMN adenylyltransferase
Similarity search - Component
Biological speciesCORYNEBACTERIUM AMMONIAGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsHerguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Medina, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms.
Authors: Herguedas, B. / Lans, I. / Sebastian, M. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M.
History
DepositionJul 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Data collection
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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 / _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: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
C: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
D: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,96218
Polymers68,5414
Non-polymers2,42214
Water5,314295
1
A: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7875
Polymers17,1351
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7875
Polymers17,1351
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6954
Polymers17,1351
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6954
Polymers17,1351
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.664, 68.664, 147.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF / RIBOFLAVIN KINASE / FLAVOKINASE / FMN ADENYLYLTRANSFERASE / FAD PYROPHOSPHORYLASE / FAD SYNTHASE


Mass: 17135.146 Da / Num. of mol.: 4 / Fragment: RIBOFLAVIN KINASE DOMAIN, UNP RESIDUES 183-338
Source method: isolated from a genetically manipulated source
Details: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL ENZYME)
Source: (gene. exp.) CORYNEBACTERIUM AMMONIAGENES (bacteria)
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q59263, riboflavin kinase, FAD synthase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTRUNCATED SEQUENCE OF CAFADS (FROM 183 TO 338 RESIDUE). RFK DOMAIN.

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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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growpH: 6.5
Details: 10-14% PEG 8000, 20% GLYCEROL, 0.1 M MES/NAOH PH 6.5, 200 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.786
11K, H, -L20.214
ReflectionResolution: 2.08→46.22 Å / Num. obs: 46431 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→37.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.597 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 258-263 IN ALL CHAINS, 325-330 IN B AND C CHAINS AND 197-203 IN A AND B CHAINS ARE DISORDERED AND NOT VISIBLE IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18869 3370 7.3 %RANDOM
Rwork0.15884 ---
obs0.16102 43014 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.161 Å2
Baniso -1Baniso -2Baniso -3
1--15.26 Å20 Å20 Å2
2---15.26 Å20 Å2
3---30.53 Å2
Refinement stepCycle: LAST / Resolution: 2.08→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 148 295 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194556
X-RAY DIFFRACTIONr_bond_other_d0.0020.024196
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9816205
X-RAY DIFFRACTIONr_angle_other_deg0.89139626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56624.366213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33515677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2741523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4873.1062211
X-RAY DIFFRACTIONr_mcbond_other1.4873.1052210
X-RAY DIFFRACTIONr_mcangle_it2.34.6372742
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6273.3282345
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 244 -
Rwork0.256 3188 -
obs--99.94 %
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)
13.49640.96060.08622.42990.58121.7969-0.0440.07660.3587-0.17280.00120.1271-0.17990.09530.04280.0551-0.0417-0.00770.13630.01330.038-14.82320.9520.47
23.22411.0848-0.12474.05090.97513.06940.0269-0.0309-0.11810.0726-0.18610.26770.4093-0.05110.15930.1506-0.03430.02750.1265-0.03860.0376-30.998-6.174-0.258
32.7382-0.2195-0.91284.21-1.19063.43020.0495-0.30290.0272-0.0388-0.2678-0.3974-0.41270.30150.21830.11670.01630.00570.23240.02740.0488-44.05235.235-13.308
42.39470.0002-0.51054.5429-1.10541.09530.00140.1414-0.4123-0.7312-0.1218-0.02140.3897-0.09970.12040.24920.01930.05270.2204-0.0210.0977-57.6646.713-12.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A185 - 501
2X-RAY DIFFRACTION2B186 - 501
3X-RAY DIFFRACTION3C186 - 501
4X-RAY DIFFRACTION4D186 - 501

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