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- PDB-2vbv: Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in co... -

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Basic information

Entry
Database: PDB / ID: 2vbv
TitleRiboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN
ComponentsRIBOFLAVIN KINASE
KeywordsTRANSFERASE / CRADLE-LOOP BARREL / CTP-DEPENDENT KINASE / FMN
Function / homology
Function and homology information


CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / nucleotide binding / magnesium ion binding
Similarity search - Function
Riboflavin kinase, archaeal / : / Riboflavin kinase domain, CTP-dependent / Riboflavin kinase, CTP-dependent / Domain of unknown function DUF120 / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / IODIDE ION / Riboflavin kinase
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHartmann, M.D. / Ammelburg, M. / Djuranovic, S. / Martin, J. / Lupas, A.N. / Zeth, K.
CitationJournal: Structure / Year: 2007
Title: A Ctp-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels.
Authors: Ammelburg, M. / Hartmann, M.D. / Djuranovic, S. / Alva, V. / Koretke, K.K. / Martin, J. / Sauer, G. / Truffault, V. / Zeth, K. / Lupas, A.N. / Coles, M.
History
DepositionSep 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOFLAVIN KINASE
B: RIBOFLAVIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8939
Polymers31,4192
Non-polymers1,4747
Water1,31573
1
A: RIBOFLAVIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7566
Polymers15,7101
Non-polymers1,0465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBOFLAVIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1373
Polymers15,7101
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.482, 73.299, 104.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RIBOFLAVIN KINASE / UNCHARACTERIZED PROTEIN MJ0056


Mass: 15709.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q60365, CTP-dependent riboflavin kinase

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Non-polymers , 6 types, 80 molecules

#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.6 Å3/Da / Density % sol: 52.8 % / Description: NONE
Crystal growDetails: 20% W/V PEG 8000, 200 MM SODIUM IODIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2141
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2141 Å / Relative weight: 1
ReflectionResolution: 2.4→38.58 Å / Num. obs: 12903 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.67
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5.62 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.25 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VBT

2vbt


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.323 644 5 %RANDOM
Rwork0.227 ---
obs0.232 12202 100 %-
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: 42.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--2.41 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 85 73 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222305
X-RAY DIFFRACTIONr_bond_other_d00.021638
X-RAY DIFFRACTIONr_angle_refined_deg1.72.0453105
X-RAY DIFFRACTIONr_angle_other_deg4.03634022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0575268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18624.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.51615447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.065158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022409
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02444
X-RAY DIFFRACTIONr_nbd_refined0.2250.2485
X-RAY DIFFRACTIONr_nbd_other0.230.21656
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21067
X-RAY DIFFRACTIONr_nbtor_other0.1140.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7571.51337
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40622171
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8143968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9514.5934
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 46
Rwork0.317 857

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