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- PDB-1zch: Structure of the hypothetical oxidoreductase YcnD from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 1zch
TitleStructure of the hypothetical oxidoreductase YcnD from Bacillus subtilis
ComponentsHypothetical oxidoreductase ycnD
KeywordsOXIDOREDUCTASE / nitroreductase / NADH-oxidase
Function / homology
Function and homology information


FMN reductase [NAD(P)H] / FMN reductase (NADH) activity / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / : / response to toxic substance
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN reductase [NAD(P)H]
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMorokutti, A. / Lyskowski, A. / Sollner, S. / Pointner, E. / Fitzpatrick, T.B. / Kratky, C. / Gruber, K. / Macheroux, P.
CitationJournal: Biochemistry / Year: 2005
Title: Structure and Function of YcnD from Bacillus subtilis, a Flavin-Containing Oxidoreductase(,).
Authors: Morokutti, A. / Lyskowski, A. / Sollner, S. / Pointner, E. / Fitzpatrick, T.B. / Kratky, C. / Gruber, K. / Macheroux, P.
History
DepositionApr 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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:
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Assembly

Deposited unit
A: Hypothetical oxidoreductase ycnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2604
Polymers28,7281
Non-polymers5323
Water4,648258
1
A: Hypothetical oxidoreductase ycnD
hetero molecules

A: Hypothetical oxidoreductase ycnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5208
Polymers57,4572
Non-polymers1,0646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12760 Å2
ΔGint-109 kcal/mol
Surface area18450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.101, 89.075, 93.608
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-428-

HOH

21A-452-

HOH

31A-453-

HOH

41A-454-

HOH

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Components

#1: Protein Hypothetical oxidoreductase ycnD


Mass: 28728.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ycnD / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P94424, Oxidoreductases
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-400, CaCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.85→18 Å / Num. all: 21381 / Num. obs: 21381 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 47
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 8.1 / Num. unique all: 1345 / Rsym value: 0.202 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BKJ

1bkj


Resolution: 1.85→17.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1909132.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1076 5 %RANDOM
Rwork0.171 ---
obs0.171 21381 99.6 %-
all-21381 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.918 Å2 / ksol: 0.36302 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2---2.06 Å20 Å2
3----0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.85→17.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 33 258 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 1.85→1.89 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.265 74 5.5 %
Rwork0.21 1281 -
obs-1345 97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5FMN.PARAMFMN.TOP

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