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- PDB-5xv5: Crystal structure of Rib7 mutant S88E from Methanosarcina mazei -

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Basic information

Entry
Database: PDB / ID: 5xv5
TitleCrystal structure of Rib7 mutant S88E from Methanosarcina mazei
ComponentsConserved protein
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
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: 2.5 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)156,8836
Polymers156,8836
Non-polymers00
Water3,837213
1
A: Conserved protein
B: Conserved protein


Theoretical massNumber of molelcules
Total (without water)52,2942
Polymers52,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-20 kcal/mol
Surface area19520 Å2
MethodPISA
2
C: Conserved protein
D: Conserved protein


Theoretical massNumber of molelcules
Total (without water)52,2942
Polymers52,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-20 kcal/mol
Surface area19050 Å2
MethodPISA
3
E: Conserved protein
F: Conserved protein


Theoretical massNumber of molelcules
Total (without water)52,2942
Polymers52,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-20 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.160, 116.160, 380.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 22313 - 235
21METMETVALVALBB1 - 22313 - 235
12ARGARGVALVALAA3 - 22315 - 235
22ARGARGVALVALCC3 - 22315 - 235
13SERSERLYSLYSAA0 - 22412 - 236
23SERSERLYSLYSDD0 - 22412 - 236
14ARGARGVALVALAA3 - 22315 - 235
24ARGARGVALVALEE3 - 22315 - 235
15METMETLYSLYSAA1 - 22613 - 238
25METMETLYSLYSFF1 - 22613 - 238
16ARGARGVALVALBB3 - 22315 - 235
26ARGARGVALVALCC3 - 22315 - 235
17METMETVALVALBB1 - 22313 - 235
27METMETVALVALDD1 - 22313 - 235
18ARGARGVALVALBB3 - 22315 - 235
28ARGARGVALVALEE3 - 22315 - 235
19METMETVALVALBB1 - 22313 - 235
29METMETVALVALFF1 - 22313 - 235
110ARGARGVALVALCC3 - 22315 - 235
210ARGARGVALVALDD3 - 22315 - 235
111ARGARGLYSLYSCC3 - 22415 - 236
211ARGARGLYSLYSEE3 - 22415 - 236
112ARGARGVALVALCC3 - 22315 - 235
212ARGARGVALVALFF3 - 22315 - 235
113ARGARGVALVALDD3 - 22315 - 235
213ARGARGVALVALEE3 - 22315 - 235
114METMETLYSLYSDD1 - 22413 - 236
214METMETLYSLYSFF1 - 22413 - 236
115ARGARGVALVALEE3 - 22315 - 235
215ARGARGVALVALFF3 - 22315 - 235

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Conserved protein


Mass: 26147.146 Da / Num. of mol.: 6 / Mutation: S88E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-25 % Tacsimate (pH 7.0), 2 % PEG 3350, 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: May 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 65992 / % possible obs: 99.8 % / Redundancy: 2.8 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.478 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUX

5xux


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.762 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28116 3183 4.8 %RANDOM
Rwork0.24624 ---
obs0.24795 62802 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å2-0 Å2
2--0.39 Å20 Å2
3----1.26 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10258 0 0 213 10471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910379
X-RAY DIFFRACTIONr_bond_other_d0.0090.0210504
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.99213938
X-RAY DIFFRACTIONr_angle_other_deg1.6324281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79451346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33124.823396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.449152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9961566
X-RAY DIFFRACTIONr_chiral_restr0.0910.21624
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211481
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022043
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_it6.3586.2145404
X-RAY DIFFRACTIONr_mcbond_other6.3586.2135403
X-RAY DIFFRACTIONr_mcangle_it9.3319.3016744
X-RAY DIFFRACTIONr_mcangle_other9.3319.3016745
X-RAY DIFFRACTIONr_scbond_it6.3456.8444975
X-RAY DIFFRACTIONr_scbond_other6.3446.8444976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7519.9787195
X-RAY DIFFRACTIONr_long_range_B_refined13.63747.52910723
X-RAY DIFFRACTIONr_long_range_B_other13.63947.52110706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A270620.08
12B270620.08
21A268280.09
22C268280.09
31A276260.08
32D276260.08
41A270560.08
42E270560.08
51A279300.07
52F279300.07
61B271040.07
62C271040.07
71B269520.08
72D269520.08
81B272400.07
82E272400.07
91B269560.08
92F269560.08
101C269720.07
102D269720.07
111C282420.02
112E282420.02
121C269480.07
122F269480.07
131D272180.07
132E272180.07
141D285520.03
142F285520.03
151E271840.07
152F271840.07
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 242 -
Rwork0.263 4674 -
obs--99.84 %

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