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- PDB-4x9m: Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumon... -

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Basic information

Entry
Database: PDB / ID: 4x9m
TitleOxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound
ComponentsL-alpha-glycerophosphate oxidase
KeywordsOXIDOREDUCTASE / flavoenzyme / oxidase / glycerol-3-phosphate oxidase / glycerol-3-phosphate dehydrogenase
Function / homology
Function and homology information


glycerol-3-phosphate oxidase / glycerol catabolic process / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
: / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...: / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / SN-GLYCEROL-3-PHOSPHATE / NICKEL (II) ION / Glycerol 3-phosphate oxidase
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsElkhal, C.K. / Kean, K.M. / Parsonage, D. / Claiborne, A. / Karplus, P.A.
CitationJournal: Febs J. / Year: 2015
Title: Structure and proposed mechanism of l-alpha-glycerophosphate oxidase from Mycoplasma pneumoniae.
Authors: Elkhal, C.K. / Kean, K.M. / Parsonage, D. / Maenpuen, S. / Chaiyen, P. / Claiborne, A. / Karplus, P.A.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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_symmetry / _struct_conn_type.id
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-alpha-glycerophosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3494
Polymers46,3321
Non-polymers1,0163
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.590, 111.590, 111.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-402-

NI

21A-568-

HOH

31A-679-

HOH

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Components

#1: Protein L-alpha-glycerophosphate oxidase


Mass: 46332.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / Gene: MPN_051, D09_orf384, MP103 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: P75063
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.68 M NaCl, 2% v/v isopropanol, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18401 / % possible obs: 100 % / Redundancy: 23.4 % / Net I/σ(I): 22.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 23.6 % / Mean I/σ(I) obs: 4.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DME

3dme


Resolution: 2.4→49.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.32 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20376 923 5 %RANDOM
Rwork0.14762 ---
obs0.15044 17440 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.397 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 64 201 3265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193174
X-RAY DIFFRACTIONr_bond_other_d0.0010.023080
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9724328
X-RAY DIFFRACTIONr_angle_other_deg0.98637085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26224.887133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23415546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5691513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02703
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4373.4861554
X-RAY DIFFRACTIONr_mcbond_other2.4353.4851553
X-RAY DIFFRACTIONr_mcangle_it3.375.2271944
X-RAY DIFFRACTIONr_mcangle_other3.375.2271945
X-RAY DIFFRACTIONr_scbond_it3.6733.8751619
X-RAY DIFFRACTIONr_scbond_other3.6733.8751619
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4945.6412382
X-RAY DIFFRACTIONr_long_range_B_refined7.17229.1373701
X-RAY DIFFRACTIONr_long_range_B_other7.11128.7923626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 58 -
Rwork0.215 1259 -
obs--98.58 %
Refinement TLS params.Method: refined / Origin x: 12.342 Å / Origin y: -25.9423 Å / Origin z: 43.7699 Å
111213212223313233
T0.0426 Å20.0216 Å2-0.0004 Å2-0.0276 Å20.0199 Å2--0.044 Å2
L0.53 °2-0.2422 °2-0.3146 °2-0.4002 °20.0808 °2--1.0753 °2
S0.0355 Å °0.0335 Å °0.016 Å °-0.0267 Å °-0.0612 Å °-0.0379 Å °0.0132 Å °0.0781 Å °0.0257 Å °

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