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- PDB-2gag: Heteroteterameric sarcosine: structure of a diflavin metaloenzyme... -

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Basic information

Entry
Database: PDB / ID: 2gag
TitleHeteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution
Components(heterotetrameric sarcosine oxidase ...) x 4
KeywordsOXIDOREDUCTASE / Sarcosine oxidase / Flavoenzyme / Electron transfer / Folate-methylating enzyme
Function / homology
Function and homology information


sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) / sarcosine catabolic process / sarcosine oxidase activity / tetrahydrofolate metabolic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family ...Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family / Sarcosine oxidase, gamma subunit family / SoxA, A3 domain / 2Fe-2S iron-sulfur cluster binding domain, N-terminal / Sarcosine oxidase A3 domain / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Rhodanese domain profile. / Rhodanese-like domain / 2Fe-2S iron-sulfur cluster binding domain / Gyrase A; domain 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / 2-FUROIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SULFITE ION / : / : / Heterotetrameric sarcosine oxidase gamma-subunit / Heterotetrameric sarcosine oxidase alpha-subunit / Heterotetrameric sarcosine oxidase delta-subunit / Sarcosine oxidase subunit beta
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, Z.W. / Hassan-Abdulah, A. / Zhao, G. / Jorns, M.S. / Mathews, F.S.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Heterotetrameric sarcosine oxidase: structure of a diflavin metalloenzyme at 1.85 a resolution.
Authors: Chen, Z.W. / Hassan-Abdulah, A. / Zhao, G. / Jorns, M.S. / Mathews, F.S.
#1: Journal: Protein Expr.Purif. / Year: 2005
Title: Cloning, expression and crystallization of heterotetrameric sarcosine oxidase from Pseudomonas maltophilia
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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: heterotetrameric sarcosine oxidase alpha-subunit
B: heterotetrameric sarcosine oxidase beta-subunit
C: heterotetrameric sarcosine oxidase gamma-subunit
D: heterotetrameric sarcosine oxidase delta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,33412
Polymers180,9674
Non-polymers2,3678
Water26,6441479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21140 Å2
ΔGint-53 kcal/mol
Surface area54070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.186, 132.407, 197.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterotetramer.

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Components

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Heterotetrameric sarcosine oxidase ... , 4 types, 4 molecules ABCD

#1: Protein heterotetrameric sarcosine oxidase alpha-subunit


Mass: 103218.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: soxA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3ZDQ8
#2: Protein heterotetrameric sarcosine oxidase beta-subunit


Mass: 44117.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: soxB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 63146664, UniProt: Q3ZDR0*PLUS
#3: Protein heterotetrameric sarcosine oxidase gamma-subunit


Mass: 22235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: soxG / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 63146667, UniProt: Q3ZDQ7*PLUS
#4: Protein heterotetrameric sarcosine oxidase delta-subunit


Mass: 11395.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: soxD / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3ZDQ9

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Non-polymers , 8 types, 1487 molecules

#5: Chemical ChemComp-FOA / 2-FUROIC ACID


Mass: 112.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4O3
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#10: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1479 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 20000, 0.1M Tris, 0.04M sodium fuorate and 0.01M sodium sulfite., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2004
RadiationMonochromator: APS BEAMLINE 14 BMC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 164316 / Num. obs: 157579 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.7 / Num. unique all: 14815 / % possible all: 91.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GAH

2gah


Resolution: 1.85→40 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1117856.93 / 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
Rfree0.23 7613 5.1 %RANDOM
Rwork0.189 ---
all-163926 --
obs-150584 91.8 %-
Displacement parametersBiso mean: 30.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12502 0 155 1479 14136
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
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
1.85-1.960.314511145.10.27652085120665
1.96-2.120.270612600.231523120
2.12-2.330.254712370.199624207
2.33-2.670.239312920.182224920
2.67-3.360.214914270.175125396
3.36-40.290.207412835.10.176424663

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