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- PDB-3hgj: Old Yellow Enzyme from Thermus scotoductus SA-01 complexed with p... -

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Basic information

Entry
Database: PDB / ID: 3hgj
TitleOld Yellow Enzyme from Thermus scotoductus SA-01 complexed with p-hydroxy-benzaldehyde
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / TIM barrel
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / Chromate reductase
Similarity search - Component
Biological speciesThermus scotoductus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsOpperman, D.J. / Sewell, B.T. / Litthauer, D. / Isupov, M.N. / Littlechild, J.A. / van Heerden, E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structure of a thermostable old yellow enzyme from Thermus scotoductus SA-01
Authors: Opperman, D.J. / Sewell, B.T. / Litthauer, D. / Isupov, M.N. / Littlechild, J.A. / van Heerden, E.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Mar 20, 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: Chromate reductase
B: Chromate reductase
C: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,41712
Polymers152,1034
Non-polymers2,3148
Water22,1581230
1
A: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2096
Polymers76,0522
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area24960 Å2
MethodPISA
2
B: Chromate reductase
hetero molecules

B: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2096
Polymers76,0522
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2460 Å2
ΔGint-13 kcal/mol
Surface area25040 Å2
MethodPISA
3
C: Chromate reductase
hetero molecules

C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2096
Polymers76,0522
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2530 Å2
ΔGint-15 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.703, 101.169, 101.336
Angle α, β, γ (deg.)90.000, 114.320, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Chromate reductase


Mass: 38025.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus (bacteria) / Strain: SA-01 / Gene: CrS / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0JDW3, NADPH dehydrogenase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1230 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35% PEG400, 0.1M Tris-HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9777 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2→33.729 Å / Num. all: 121277 / Num. obs: 121277 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.11 / Rrim(I) all: 0.212 / Rsym value: 0.181 / Net I/av σ(I): 3.038 / Net I/σ(I): 8.2 / Num. measured all: 419177
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.20.670.564155501173600.360.670.5641.597
2.11-2.243.20.4720.3981.853608165170.250.470.3982.298.3
2.24-2.393.30.3770.3182.352404156500.20.380.3183.298.8
2.39-2.583.50.2980.2532.851093146610.160.30.2534.899.4
2.58-2.833.60.2490.2133.249171135620.130.250.2136.999.7
2.83-3.163.70.2170.1873.645758123170.110.220.1879.599.9
3.16-3.653.70.180.1554.140039108710.090.180.15514.499.9
3.65-4.473.60.1530.1314.63278891880.080.150.13119.9100
4.47-6.323.50.1410.124.62530071780.070.140.1222.2100
6.32-67.273.40.1170.0994.71351539730.060.120.09925.599.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.729 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.526 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 6128 5.1 %RANDOM
Rwork0.199 115143 --
obs0.202 121271 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.44 Å2 / Biso mean: 21.853 Å2 / Biso min: 2.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20.59 Å2
2---0.07 Å20 Å2
3----0.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: LAST / Resolution: 2→33.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10696 0 160 1230 12086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211183
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.00815239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93551401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71121.734467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.697151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.32315129
X-RAY DIFFRACTIONr_chiral_restr0.10.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0228597
X-RAY DIFFRACTIONr_mcbond_it1.0521.56941
X-RAY DIFFRACTIONr_mcangle_it1.677211114
X-RAY DIFFRACTIONr_scbond_it3.04634242
X-RAY DIFFRACTIONr_scangle_it4.5444.54118
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 437 -
Rwork0.316 8307 -
all-8744 -
obs--96.75 %

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