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- PDB-1hdr: THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCT... -

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Basic information

Entry
Database: PDB / ID: 1hdr
TitleTHE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCTASE NADH BINARY COMPLEX EXPRESSED IN ESCHERICHIA COLI BY A CDNA CONSTRUCTED FROM ITS RAT HOMOLOGUE
ComponentsDIHYDROPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE(ACTING ON NADH)
Function / homology
Function and homology information


dihydrobiopterin metabolic process / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / Phenylalanine metabolism / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / amino acid metabolic process / NADPH binding / electron transfer activity ...dihydrobiopterin metabolic process / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / Phenylalanine metabolism / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / amino acid metabolic process / NADPH binding / electron transfer activity / mitochondrion / extracellular exosome / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsVarughese, K.I. / Su, Y. / Xuong, N.H. / Whiteley, J.M.
CitationJournal: J.Biol.Chem. / Year: 1993
Title: The crystallographic structure of a human dihydropteridine reductase NADH binary complex expressed in Escherichia coli by a cDNA constructed from its rat homologue.
Authors: Su, Y. / Varughese, K.I. / Xuong, N.H. / Bray, T.L. / Roche, D.J. / Whiteley, J.M.
History
DepositionAug 18, 1993Processing site: BNL
Revision 1.0Aug 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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

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Assembly

Deposited unit
A: DIHYDROPTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4802
Polymers25,8161
Non-polymers6631
Water1,63991
1
A: DIHYDROPTERIDINE REDUCTASE
hetero molecules

A: DIHYDROPTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9604
Polymers51,6332
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5900 Å2
ΔGint-44 kcal/mol
Surface area18700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.650, 138.650, 65.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DIHYDROPTERIDINE REDUCTASE


Mass: 25816.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / References: UniProt: P09417, EC: 1.6.99.7
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DHPR_HUMAN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE THR 51 SER 50 PLEASE NOTE THAT THE SWISS-PROT ENTRY IS BASED ON LOCKYER ET AL. (1987) PNAS 84, 3329. THE SEQUENCE USED IN THIS ENTRY IS IDENTICAL TO THAT IN DAHL ET AL. (1987) NUCLEIC ACIDS RES. 15, 1921.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
28 %methanol1reservoir
31 mMbeta-mercaptoethanol1reservoir
1PEG45001reservoir
4Tris phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 7999 / % possible obs: 97 % / Redundancy: 4.8 % / Num. measured all: 38602 / Rmerge(I) obs: 0.0736
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.69 Å / Num. unique obs: 1451 / Num. measured obs: 3355 / Rmerge(I) obs: 0.1802

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.169 / Rfactor obs: 0.169 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 44 91 1902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.2
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: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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