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- PDB-1dir: CRYSTAL STRUCTURE OF A MONOCLINIC FORM OF DIHYDROPTERIDINE REDUCT... -

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Basic information

Entry
Database: PDB / ID: 1dir
TitleCRYSTAL STRUCTURE OF A MONOCLINIC FORM OF DIHYDROPTERIDINE REDUCTASE FROM RAT LIVER
ComponentsDIHYDROPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE(ACTING ON NADH OR NADPH)
Function / homology
Function and homology information


Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / response to aluminum ion / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / response to glucagon / NADPH binding / liver development ...Phenylalanine metabolism / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / response to aluminum ion / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / response to glucagon / NADPH binding / liver development / response to lead ion / cellular response to xenobiotic stimulus / identical protein binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydropteridine reductase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsVarughese, K.I. / Su, Y. / Skinner, M.M. / Matthews, D.A. / Whitely, J.M. / Xuong, N.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystal structure of a monoclinic form of dihydropteridine reductase from rat liver.
Authors: Su, Y. / Skinner, M.M. / Xuong, N.H. / Matthews, D.A. / Whiteley, J.M. / Varughese, K.I.
History
DepositionApr 18, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 12, 2014Group: Refinement description
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DIHYDROPTERIDINE REDUCTASE
B: DIHYDROPTERIDINE REDUCTASE
C: DIHYDROPTERIDINE REDUCTASE
D: DIHYDROPTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9708
Polymers102,3174
Non-polymers2,6544
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIHYDROPTERIDINE REDUCTASE
D: DIHYDROPTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4854
Polymers51,1582
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-43 kcal/mol
Surface area18450 Å2
MethodPISA
3
A: DIHYDROPTERIDINE REDUCTASE
B: DIHYDROPTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4854
Polymers51,1582
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-40 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.200, 46.500, 94.300
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: MET C 190 - PRO C 191 OMEGA = 215.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein
DIHYDROPTERIDINE REDUCTASE


Mass: 25579.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P11348, EC: 1.6.99.7
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.8 / Method: vapor diffusion, hanging drop / Details: referred to 1dhr
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 %(w/v)PEG45001reservoir
20.05 MTris-HCl1reservoir
311 %(v/v)ethanol1reservoir
410 mg/mlprotein NADH solution1drop0.005ml
517 %(w/v)PEG45001drop
611 %(v/v)ethanol1drop
70.05 MTris-HCl1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 5.13 Å / Num. measured all: 26789 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / % possible obs: 54.7 % / Num. measured obs: 3187 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.168 -
obs-29023
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7048 0 176 148 7372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.5

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