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- PDB-2bd0: Chlorobium tepidum Sepiapterin Reductase complexed with NADP and ... -

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Basic information

Entry
Database: PDB / ID: 2bd0
TitleChlorobium tepidum Sepiapterin Reductase complexed with NADP and Sepiapterin
Componentssepiapterin reductase
KeywordsOXIDOREDUCTASE / sepiapterin reductase / Chlorobium tepidum
Function / homology
Function and homology information


sepiapterin reductase (L-threo-7,8-dihydrobiopterin forming) / oxidoreductase activity / nucleotide binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / 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
BIOPTERIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Sepiapterin reductase
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSupangat, S. / Seo, K.H. / Choi, Y.K. / Park, Y.S. / Lee, K.H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of Chlorobium tepidum sepiapterin reductase complex reveals the novel substrate binding mode for stereospecific production of L-threo-tetrahydrobiopterin
Authors: Supangat, S. / Seo, K.H. / Choi, Y.K. / Park, Y.S. / Son, D. / Han, C.D. / Lee, K.H.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 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: sepiapterin reductase
B: sepiapterin reductase
C: sepiapterin reductase
D: sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8009
Polymers108,5894
Non-polymers3,2115
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16330 Å2
ΔGint-85 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.359, 97.482, 123.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer of the tetramer in the asymmetric unit.

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Components

#1: Protein
sepiapterin reductase /


Mass: 27147.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8KES3, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-BIO / BIOPTERIN / Biopterin


Mass: 237.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M tris, 34% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 6B11.1273
SYNCHROTRONPhoton Factory BL-6A20.978, 0.97934, 0.97035
Detector
TypeIDDetectorDate
BRUKER1CCDDec 14, 2004
BRUKER2CCDDec 14, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.12731
20.9781
30.979341
40.970351
ReflectionResolution: 1.7→31.9 Å / Num. obs: 111871 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.3
Reflection shellResolution: 1.7→1.81 Å / Rmerge(I) obs: 0.519 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→31.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5630 5 %RNDOM
Rwork0.2 ---
obs-111871 99.8 %-
Solvent computationBsol: 51.455 Å2
Displacement parametersBiso mean: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.273 Å20 Å20 Å2
2---3.826 Å20 Å2
3---6.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.019 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 209 369 7974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection
Rfree0.271 912
Rwork0.252 -
obs-17572
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2NADP.param
X-RAY DIFFRACTION3BIO_xplor.param
X-RAY DIFFRACTION4water_rep.param

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