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- PDB-1rhc: F420-dependent secondary alcohol dehydrogenase in complex with an... -

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Basic information

Entry
Database: PDB / ID: 1rhc
TitleF420-dependent secondary alcohol dehydrogenase in complex with an F420-acetone adduct
ComponentsF420-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / (alpha / beta)8 barrel
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
Similarity search - Function
F420-dependent glucose-6-phosphate dehydrogenase-related / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETONE / COENZYME F420 / : / : / F420-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesMethanoculleus thermophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsAufhammer, S.W. / Warkentin, E. / Berk, H. / Shima, S. / Thauer, R.K. / Ermler, U.
CitationJournal: Structure / Year: 2004
Title: Coenzyme binding in f(420)-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family.
Authors: Aufhammer, S.W. / Warkentin, E. / Berk, H. / Shima, S. / Thauer, R.K. / Ermler, U.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: F420-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1416
Polymers37,2001
Non-polymers9425
Water2,630146
1
A: F420-dependent alcohol dehydrogenase
hetero molecules

A: F420-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,28312
Polymers74,3992
Non-polymers1,88310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8250 Å2
ΔGint-59 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.824, 156.316, 60.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-557-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: 1-x, y, 1/2-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein F420-dependent alcohol dehydrogenase


Mass: 37199.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanoculleus thermophilus (archaea)
References: GenBank: 4225975, UniProt: O93734*PLUS, EC: 1.1.99.-

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-F42 / COENZYME F420 / Coenzyme F420


Mass: 773.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N5O18P
#5: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 7

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 8000, sodium chloride, sodium citrate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.04 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 2003 / Details: double focussing
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. all: 45082 / Num. obs: 45082 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.33 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→19.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1535570.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1901 5 %RANDOM
Rwork0.158 ---
obs0.158 38086 99.2 %-
all-38086 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2308 Å2 / ksol: 0.346185 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---4.03 Å20 Å2
3---4.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 56 150 2816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 332 5.3 %
Rwork0.201 5947 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADH_CIS.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMNAP_F42.TOP
X-RAY DIFFRACTION5NAP_F42.PAR

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