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- PDB-3hf3: Old Yellow Enzyme from Thermus scotoductus SA-01 -

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Basic information

Entry
Database: PDB / ID: 3hf3
TitleOld Yellow Enzyme from Thermus scotoductus SA-01
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 / Chromate reductase
Similarity search - Component
Biological speciesThermus scotoductus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 11, 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 / pdbx_struct_special_symmetry / 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)154,31312
Polymers152,1034
Non-polymers2,2108
Water15,277848
1
A: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1576
Polymers76,0522
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15 kcal/mol
Surface area24910 Å2
MethodPISA
2
B: Chromate reductase
hetero molecules

B: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1576
Polymers76,0522
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2520 Å2
ΔGint-14 kcal/mol
Surface area25100 Å2
MethodPISA
3
C: Chromate reductase
hetero molecules

C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1576
Polymers76,0522
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2530 Å2
ΔGint-16 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.780, 101.880, 180.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-915-

HOH

21C-895-

HOH

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
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: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.733
11K, H, -L20.267
ReflectionResolution: 2.2→38.282 Å / Num. all: 90706 / Num. obs: 90706 / % possible obs: 94.7 % / Redundancy: 4.6 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.146 / Rsym value: 0.13 / Num. measured all: 419764
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9739 / % possible all: 90.6

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.101 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4542 5 %RANDOM
Rwork0.174 86122 --
obs0.176 90664 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.15 Å2 / Biso mean: 23.285 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å20 Å2
2---7.93 Å20 Å2
3---13.57 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10696 0 144 848 11688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211111
X-RAY DIFFRACTIONr_angle_refined_deg1.362.00715143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46851390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25521.844461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.79215124
X-RAY DIFFRACTIONr_chiral_restr0.1020.21661
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0228512
X-RAY DIFFRACTIONr_mcbond_it1.4871.56923
X-RAY DIFFRACTIONr_mcangle_it2.307211078
X-RAY DIFFRACTIONr_scbond_it4.11134188
X-RAY DIFFRACTIONr_scangle_it5.9964.54064
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 276 -
Rwork0.192 5645 -
all-5921 -
obs--84.49 %

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