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- PDB-2raf: Crystal structure of putative dinucleotide-binding oxidoreductase... -

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Basic information

Entry
Database: PDB / ID: 2raf
TitleCrystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from Lactobacillus plantarum at 1.60 A resolution
ComponentsPutative Dinucleotide-Binding Oxidoreductase
KeywordsOXIDOREDUCTASE / NP_786167.1 / Putative Dinucleotide-Binding Oxidoreductase / NADP oxidoreductase coenzyme F420-dependent / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Oxidoreductase / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from Lactobacillus plantarum at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG WHICH WAS NOT ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG WHICH WAS NOT CLEAVED AFTER PURIFICATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Dinucleotide-Binding Oxidoreductase
B: Putative Dinucleotide-Binding Oxidoreductase
C: Putative Dinucleotide-Binding Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0115
Polymers69,1623
Non-polymers8502
Water11,151619
1
A: Putative Dinucleotide-Binding Oxidoreductase
B: Putative Dinucleotide-Binding Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8513
Polymers46,1082
Non-polymers7431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
MethodPISA
2
C: Putative Dinucleotide-Binding Oxidoreductase
hetero molecules

C: Putative Dinucleotide-Binding Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3204
Polymers46,1082
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area3010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.330, 152.570, 140.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-236-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative Dinucleotide-Binding Oxidoreductase


Mass: 23053.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarum / Strain: WCFS1, NCIMB 8826 / Gene: NP_786167.1, lp_2792 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q88TW8, UniProt: F9URQ8*PLUS, Oxidoreductases
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 20.0% PEG 3350, 0.2M Ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97886, 0.97917
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978861
30.979171
ReflectionResolution: 1.6→29.54 Å / Num. obs: 75349 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.872 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.660.3682.2232291498698.5
1.66-1.720.3032.7207681324399.8
1.72-1.80.2463.3233401485499.7
1.8-1.90.1774.5243531530899.7
1.9-2.020.1286.2232921453599.5
2.02-2.170.0898.7224461390299.5
2.17-2.390.06411.7239051460399.6
2.39-2.730.04914.9237331433299.5
2.73-3.440.03121.5244191458299.3
3.44-29.540.0232.7247341431197.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.444 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ONE PEG MOLECULE HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3791 5 %RANDOM
Rwork0.151 ---
obs0.153 75306 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 48 626 5217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224704
X-RAY DIFFRACTIONr_bond_other_d0.0040.023039
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9666420
X-RAY DIFFRACTIONr_angle_other_deg1.4237535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5995630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16326.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.46115796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.5441510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025315
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02859
X-RAY DIFFRACTIONr_nbd_refined0.20.3870
X-RAY DIFFRACTIONr_nbd_other0.1570.33146
X-RAY DIFFRACTIONr_nbtor_refined0.1750.52293
X-RAY DIFFRACTIONr_nbtor_other0.0850.52301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.5836
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1340.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.326
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.578
X-RAY DIFFRACTIONr_mcbond_it2.22733239
X-RAY DIFFRACTIONr_mcbond_other0.53231224
X-RAY DIFFRACTIONr_mcangle_it2.78954799
X-RAY DIFFRACTIONr_scbond_it4.51281884
X-RAY DIFFRACTIONr_scangle_it6.387111600
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 277 -
Rwork0.187 5170 -
all-5447 -
obs--99.22 %

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