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- PDB-1eli: COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE... -

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Basic information

Entry
Database: PDB / ID: 1eli
TitleCOMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATE
ComponentsSARCOSINE OXIDASE
KeywordsOXIDOREDUCTASE / flavoprotein / oxidase
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / PYRROLE-2-CARBOXYLATE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWagner, M.A. / Trickey, P. / Chen, Z.-W. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2000
Title: Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants.
Authors: Wagner, M.A. / Trickey, P. / Chen, Z.W. / Mathews, F.S. / Jorns, M.S.
#1: Journal: Structure / Year: 1999
Title: Monomeric Sarcosine Oxidase: Structure of a Covalently Flavinylated Amine Oxidizing Enzyme
Authors: Trickey, P. / Wagner, M.A. / Jorns, M.S. / Mathews, F.S.
History
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SARCOSINE OXIDASE
B: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,11612
Polymers86,8592
Non-polymers2,25710
Water11,746652
1
A: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4565
Polymers43,4301
Non-polymers1,0264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6617
Polymers43,4301
Non-polymers1,2316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.825, 69.360, 73.737
Angle α, β, γ (deg.)90.00, 94.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is monomer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SARCOSINE OXIDASE


Mass: 43429.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: B-0618 / Cell (production host): DH1 CELLS / Production host: Escherichia coli (E. coli)
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)

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Non-polymers , 5 types, 662 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.46 %
Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were ...Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were used for the experiments since they were the only ones on hand at the time. Kinetic studies showed that the presence of selenomethionine had little effect.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: phosphate, tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
pH: 8
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
220 mMTris-HCl1drop
32.1 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→500 Å / Num. all: 49517 / Num. obs: 44120 / % possible obs: 89.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.33 / Num. unique all: 1176 / % possible all: 47.2
Reflection shell
*PLUS
% possible obs: 47.2 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
SCALEPACKdata scaling
RefinementResolution: 2→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4393 -RANDOM
Rwork0.163 ---
obs0.163 43191 86.9 %-
all-49705 --
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 147 652 6815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7

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