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- PDB-6p8c: 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate redu... -

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Basic information

Entry
Database: PDB / ID: 6p8c
Title2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus
Components2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
KeywordsOXIDOREDUCTASE / Riboflavin / Cofactor / Methanothermobacter thermautotrophicus.
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 speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsCarbone, V. / Schofield, L.R. / Hannus, I. / Sutherland-Smith, A.J. / Ronimus, R.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other government New Zealand
CitationJournal: To Be Published
Title: The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus
Authors: Carbone, V. / Schofield, L.R. / Hannus, I. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
B: 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,74511
Polymers54,7952
Non-polymers1,9509
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: UTILIZED PISA ANALYSIS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.921, 89.597, 107.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.123043, 0.006945, -0.992377), (0.000161, -0.999976, -0.006979), (-0.992401, 0.000699, -0.123041)133.266846, 37.004261, 150.921509

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase / DARP reductase / 2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase / 5- ...DARP reductase / 2 / 5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase / 5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthase / DARIPP synthase


Mass: 27397.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_235 / Production host: Escherichia coli (E. coli)
References: UniProt: O26337, 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M magnesium chloride, 10% (w/v) PEG 8000, 0.1 M Na-Cacodylate pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.07→68.698 Å / Num. all: 34024 / Num. obs: 34024 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.112 / Rsym value: 0.1 / Net I/av σ(I): 5.4 / Net I/σ(I): 10.1 / Num. measured all: 179331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.07-2.185.30.68412599448650.3320.7630.6842.599.4
2.18-2.315.30.4871.22445546080.2410.5460.4873.799.6
2.31-2.475.40.2952.62359143940.1410.3280.2955.199.8
2.47-2.675.30.2023.62154440410.0980.2250.2027.299.8
2.67-2.935.30.1364.91999937550.0660.1520.1369.799.9
2.93-3.275.30.0848.51825834480.040.0930.08413.4100
3.27-3.785.20.0737.41597430580.0360.0820.07318.1100
3.78-4.635.10.0579.71329925890.0280.0640.05721.2100
4.63-6.5550.04612.21040420610.0230.0510.04621.299.9
6.55-45.9384.80.04110.8581312050.0220.0460.04122.299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.94 Å
Translation2.5 Å45.94 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.20data scaling
PHASER2.5.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AZN
Resolution: 2.07→45.981 Å / SU R Cruickshank DPI: 0.1685 / Cross valid method: THROUGHOUT / Details: UTILIZED TLS REFINEMENT FOR FINAL CYCLE
RfactorNum. reflection% reflection
Rfree0.22168 1724 5.1 %
Rwork0.17051 --
obs0.17317 32245 99.6451 %
Displacement parametersBiso max: 92.41 Å2 / Biso mean: 38.9059 Å2 / Biso min: 18.65 Å2
Refinement stepCycle: LAST / Resolution: 2.07→45.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 123 267 3684

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