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- PDB-3kox: Crystal Structure of ornithine 4,5 aminomutase in complex with 2,... -

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Basic information

Entry
Database: PDB / ID: 3kox
TitleCrystal Structure of ornithine 4,5 aminomutase in complex with 2,4-diaminobutyrate (Anaerobic)
Components(D-ornithine aminomutase ...) x 2
KeywordsMETAL BINDING PROTEIN / D-ornithine 4 / 5 aminomutase (OAM) / 2 / 4-diaminobutyrate (DAB) complex / Anaerobic
Function / homology
Function and homology information


D-ornithine 4,5-aminomutase / D-ornithine 4,5-aminomutase activity / cobalamin binding / protein dimerization activity / metal ion binding
Similarity search - Function
Ornithine 4,5 aminomutase S component, alpha subunit-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2220 / D-ornithine 4,5-aminomutase alpha-subunit / D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain / D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily / D-Lysine 5,6-aminomutase alpha subunit superfamily / D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit ...Ornithine 4,5 aminomutase S component, alpha subunit-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2220 / D-ornithine 4,5-aminomutase alpha-subunit / D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain / D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily / D-Lysine 5,6-aminomutase alpha subunit superfamily / D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit / Dimerisation domain of d-ornithine 4,5-aminomutase / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Defensin A-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / Chem-Z98 / D-ornithine 4,5-aminomutase subunit beta / D-ornithine 4,5-aminomutase subunit alpha / D-ornithine 4,5-aminomutase subunit beta / D-ornithine 4,5-aminomutase subunit alpha
Similarity search - Component
Biological speciesClostridium sticklandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsWolthers, K.R. / Levy, C.W. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.
Authors: Wolthers, K.R. / Levy, C. / Scrutton, N.S. / Leys, D.
History
DepositionNov 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: D-ornithine aminomutase E component
E: D-ornithine aminomutase S component
B: D-ornithine aminomutase E component
F: D-ornithine aminomutase S component
C: D-ornithine aminomutase E component
G: D-ornithine aminomutase S component
D: D-ornithine aminomutase E component
H: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,94820
Polymers396,2328
Non-polymers7,71512
Water14,178787
1
A: D-ornithine aminomutase E component
E: D-ornithine aminomutase S component
C: D-ornithine aminomutase E component
G: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,97410
Polymers198,1164
Non-polymers3,8586
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29700 Å2
ΔGint-193 kcal/mol
Surface area57320 Å2
MethodPISA
2
B: D-ornithine aminomutase E component
F: D-ornithine aminomutase S component
D: D-ornithine aminomutase E component
H: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,97410
Polymers198,1164
Non-polymers3,8586
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29980 Å2
ΔGint-198 kcal/mol
Surface area57080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.960, 231.690, 123.890
Angle α, β, γ (deg.)90.00, 103.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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D-ornithine aminomutase ... , 2 types, 8 molecules ABCDEFGH

#1: Protein
D-ornithine aminomutase E component


Mass: 85412.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sticklandii (bacteria) / Gene: oraE / Plasmid: Pet23d / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue Stratagene / References: UniProt: Q8VPJ5, UniProt: E3PY95*PLUS
#2: Protein
D-ornithine aminomutase S component


Mass: 13645.780 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sticklandii (bacteria) / Gene: oraS / Plasmid: Pet23d / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue Stratagene / References: UniProt: Q8VPJ6, UniProt: E3PY96*PLUS

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Non-polymers , 4 types, 799 molecules

#3: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Chemical
ChemComp-Z98 / (2S)-2-amino-4-{[(1Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}butanoic acid


Mass: 347.261 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18N3O7P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE STRUCTURE DOES NOT CONTAIN RESIDUES GLY220 TO ASP222 OF ORAE PRESENT IN THE UNP SEQUENCE. WE DO ...THE STRUCTURE DOES NOT CONTAIN RESIDUES GLY220 TO ASP222 OF ORAE PRESENT IN THE UNP SEQUENCE. WE DO NOT FIND ANY EVIDENCE FOR THESE RESIDUES FROM CLOSTRIDIUM STICKLANDII GENOMIC DNA SEQUENCING OR BY ALIGNMENT BETWEEN THE ORAE PROTEIN SEQUENCES FROM CLOSTRIDIUM STICKLANDII AND CLOSTRIDIUM DIFFICILE (ACCESSION NUMBER ZP_05349629; 79% SEQUENCE IDENTITY) WHICH ALSO SHOWS THAT THE CORRESPONDING ORAE CODING SEQUENCE FROM THE LATTER ORGANISM ALSO DOES NOT CONTAIN THE THREE AMINO ACID GID INSERT (A SIMILAR CONCLUSION CAN BE REACHED BY ALIGNMENT WITH VARIOUS THERMOANAEROBACTER SP)

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 294 K / pH: 8
Details: A protein solution (8 mg/ml 4,5-OAM, 5 mM 2-mercaptoethanol, 10 mM Tris HCl pH 8.0, 2 mM PLP, and 2 mM AdoCbl) was mixed in a 1:1 ratio with precipitant solution [(0.1 M Tris HCl, pH 8.0, 0. ...Details: A protein solution (8 mg/ml 4,5-OAM, 5 mM 2-mercaptoethanol, 10 mM Tris HCl pH 8.0, 2 mM PLP, and 2 mM AdoCbl) was mixed in a 1:1 ratio with precipitant solution [(0.1 M Tris HCl, pH 8.0, 0.2 M MgCl2, 25% (wt/vol) polyethylene glycol 2000 mono-methylether] under redlight at room temperature, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2009
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.4→65 Å / Num. obs: 133606 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→64.23 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.088 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 7055 5 %RANDOM
Rwork0.19 ---
obs0.193 133606 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.24 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26064 0 528 787 27379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02227124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218386
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.98836800
X-RAY DIFFRACTIONr_angle_other_deg0.988344788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74653332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83524.2981203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.637154722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.90615191
X-RAY DIFFRACTIONr_chiral_restr0.1850.24121
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02129991
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025292
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_it0.6661.516656
X-RAY DIFFRACTIONr_mcbond_other0.1371.56804
X-RAY DIFFRACTIONr_mcangle_it1.245226807
X-RAY DIFFRACTIONr_scbond_it2.03310468
X-RAY DIFFRACTIONr_scangle_it3.2814.59993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 519 -
Rwork0.275 9888 -
obs--99.87 %

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