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- PDB-5xv0: Crystal structure of Rib7 mutant D33N from Methanosarcina mazei -

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Basic information

Entry
Database: PDB / ID: 5xv0
TitleCrystal structure of Rib7 mutant D33N from Methanosarcina mazei
ComponentsConserved proteinConservation
KeywordsOXIDOREDUCTASE / Rib7 / riboflavin biosynthesis
Function / homology
Function and homology information


2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding
Similarity search - Function
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase, archaeal / Riboflavin-specific deaminase, C-terminal / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYeh, T.M. / Chen, S.C. / Chang, T.H. / Huang, M.F. / Liaw, S.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Evolution of archaeal Rib7 and eubacterial RibG reductases in riboflavin biosynthesis: Substrate specificity and cofactor preference.
Authors: Chen, S.C. / Yen, T.M. / Chang, T.H. / Liaw, S.H.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved protein
B: Conserved protein
C: Conserved protein
D: Conserved protein
E: Conserved protein
F: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,08512
Polymers156,6256
Non-polymers4,4606
Water12,592699
1
A: Conserved protein
B: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6954
Polymers52,2082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-28 kcal/mol
Surface area18970 Å2
MethodPISA
2
C: Conserved protein
D: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6954
Polymers52,2082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-32 kcal/mol
Surface area18560 Å2
MethodPISA
3
E: Conserved protein
F: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6954
Polymers52,2082
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-29 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.098, 117.098, 380.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein
Conserved protein / Conservation


Mass: 26104.125 Da / Num. of mol.: 6 / Mutation: D33N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: MM_0826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PYN5
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 % Tacsimate (pH 7.0), 10 % PEG 5000, and 100 mM HEPES (pH 7.0)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 141352 / % possible obs: 99.9 % / Redundancy: 5.8 % / Net I/σ(I): 22.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.652 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUX

5xux


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.783 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28874 6953 4.9 %RANDOM
Rwork0.24167 ---
obs0.24397 134334 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.209 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å2-0 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10403 0 288 699 11390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910847
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210607
X-RAY DIFFRACTIONr_angle_refined_deg1.5432.01914630
X-RAY DIFFRACTIONr_angle_other_deg0.94324620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86451365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16724.617405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.605152041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0791567
X-RAY DIFFRACTIONr_chiral_restr0.0780.21689
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211722
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022047
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_it2.7244.2315478
X-RAY DIFFRACTIONr_mcbond_other2.7244.2315477
X-RAY DIFFRACTIONr_mcangle_it4.2366.3296837
X-RAY DIFFRACTIONr_mcangle_other4.2366.336838
X-RAY DIFFRACTIONr_scbond_it2.7474.6415369
X-RAY DIFFRACTIONr_scbond_other2.7474.6415370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4236.8157794
X-RAY DIFFRACTIONr_long_range_B_refined11.1351.50811749
X-RAY DIFFRACTIONr_long_range_B_other11.1351.4811732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 470 -
Rwork0.296 9797 -
obs--98.47 %

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