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- PDB-2gf3: Structure of the complex of monomeric sarcosine with its substrat... -

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Basic information

Entry
Database: PDB / ID: 2gf3
TitleStructure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / INHIBITOR 2-FUROIC ACID
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 / 2-FUROIC ACID / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChen, Z. / Trickey, P. / Jorns, M.S. / Mathews, F.S.
Citation
Journal: TO BE PUBLISHED
Title: Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.
Authors: Chen, Z. / Trickey, P. / Jorns, M.S. / Mathews, F.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 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 28, 2012Group: Non-polymer description
Revision 1.4Aug 30, 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 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monomeric sarcosine oxidase
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,76215
Polymers86,2032
Non-polymers2,55913
Water17,871992
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3347
Polymers43,1011
Non-polymers1,2326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4298
Polymers43,1011
Non-polymers1,3277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.727, 69.440, 73.671
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Monomeric sarcosine oxidase / MSOX


Mass: 43101.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: soxA, sox / Plasmid: B-0618 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)

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Non-polymers , 6 types, 1005 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#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-FOA / 2-FUROIC ACID


Mass: 112.083 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.8-2.1M Sodium/potassium phosphate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 178944 / Num. obs: 170534 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20
Reflection shellHighest resolution: 1.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 1.9 / % possible all: 82.4

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L9F

1l9f
PDB Unreleased entry


Resolution: 1.3→14.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1532946.36 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 16587 10 %RANDOM
Rwork0.17 ---
all-179353 --
obs-165773 92.5 %-
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å2-1.19 Å2
2--0.28 Å20 Å2
3---2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 167 992 7175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
1.3-1.380.2219252710.10.21222246622430
1.38-1.490.209828050.184625118
1.49-1.640.189129230.160225935
1.64-1.870.181929600.154726612
1.87-2.360.173629490.151926810
2.36-14.980.2114242310.10.18392246622281

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