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

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Basic information

Entry
Database: PDB / ID: 3koy
TitleCrystal Structure of ornithine 4,5 aminomutase in complex with ornithine (Aerobic)
Components
  • D-ornithine aminomutase E component
  • D-ornithine aminomutase S component
KeywordsMETAL BINDING PROTEIN / D-ornithine 4 / 5 aminomutase (OAM) / Ornithine complex / Aerobic
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-Z97 / 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: 2.8 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 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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_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_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_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: 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)404,00420
Polymers396,2328
Non-polymers7,77212
Water0
1
A: D-ornithine aminomutase E component
E: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0015
Polymers99,0582
Non-polymers1,9433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-41 kcal/mol
Surface area35890 Å2
MethodPISA
2
D: D-ornithine aminomutase E component
H: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0015
Polymers99,0582
Non-polymers1,9433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-42 kcal/mol
Surface area35900 Å2
MethodPISA
3
C: D-ornithine aminomutase E component
G: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0015
Polymers99,0582
Non-polymers1,9433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-44 kcal/mol
Surface area35870 Å2
MethodPISA
4
B: D-ornithine aminomutase E component
F: D-ornithine aminomutase S component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0015
Polymers99,0582
Non-polymers1,9433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-42 kcal/mol
Surface area35840 Å2
MethodPISA
5
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)202,00210
Polymers198,1164
Non-polymers3,8866
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24490 Å2
ΔGint-181 kcal/mol
Surface area58750 Å2
MethodPISA
6
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)202,00210
Polymers198,1164
Non-polymers3,8866
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24800 Å2
ΔGint-182 kcal/mol
Surface area58610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.520, 233.220, 124.140
Angle α, β, γ (deg.)90.00, 103.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical
ChemComp-Z97 / (E)-N~5~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-ornithine


Mass: 361.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H20N3O7P
#5: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / 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 red light 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 Å
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: 2.8→120.75 Å / Num. all: 84568 / % possible obs: 93.81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.6 / % possible all: 87.04

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
DNAdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→60.373 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.876 / SU ML: 0.44 / σ(F): 1.36 / Phase error: 27.91 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2625 4264 5.05 %
Rwork0.1834 --
obs0.1874 84502 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.003 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 38.129 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-1.57 Å2
2--1.92 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→60.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26060 0 532 0 26592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01227116
X-RAY DIFFRACTIONf_angle_d1.41836789
X-RAY DIFFRACTIONf_dihedral_angle_d20.83210207
X-RAY DIFFRACTIONf_chiral_restr0.1154116
X-RAY DIFFRACTIONf_plane_restr0.0064753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.32781250.23672452X-RAY DIFFRACTION88
2.8318-2.86510.33331390.25712509X-RAY DIFFRACTION87
2.8651-2.90010.35891460.24412414X-RAY DIFFRACTION84
2.9001-2.93680.37941400.25622457X-RAY DIFFRACTION88
2.9368-2.97540.31571230.2382527X-RAY DIFFRACTION89
2.9754-3.01620.37071070.22812551X-RAY DIFFRACTION87
3.0162-3.05930.30381310.23012468X-RAY DIFFRACTION89
3.0593-3.10490.32641300.2282597X-RAY DIFFRACTION90
3.1049-3.15350.35061200.22532592X-RAY DIFFRACTION90
3.1535-3.20520.30311270.22172543X-RAY DIFFRACTION90
3.2052-3.26040.3211400.21872656X-RAY DIFFRACTION93
3.2604-3.31970.33231420.21112641X-RAY DIFFRACTION91
3.3197-3.38350.30871370.20772602X-RAY DIFFRACTION93
3.3835-3.45260.29661550.19172719X-RAY DIFFRACTION95
3.4526-3.52770.29821500.18322708X-RAY DIFFRACTION94
3.5277-3.60970.2661320.16762704X-RAY DIFFRACTION96
3.6097-3.70.25111410.16442735X-RAY DIFFRACTION95
3.7-3.80.24491450.15832741X-RAY DIFFRACTION97
3.8-3.91180.23521620.16122774X-RAY DIFFRACTION97
3.9118-4.0380.24581540.15272754X-RAY DIFFRACTION98
4.038-4.18230.24821600.14992796X-RAY DIFFRACTION97
4.1823-4.34970.20051500.14152794X-RAY DIFFRACTION99
4.3497-4.54760.1931620.13652791X-RAY DIFFRACTION98
4.5476-4.78730.23021440.13642818X-RAY DIFFRACTION98
4.7873-5.08710.20341610.15052809X-RAY DIFFRACTION99
5.0871-5.47960.27111400.15722827X-RAY DIFFRACTION98
5.4796-6.03060.24331570.1682809X-RAY DIFFRACTION98
6.0306-6.90220.22831480.15562758X-RAY DIFFRACTION97
6.9022-8.69190.18081410.13572866X-RAY DIFFRACTION100
8.6919-60.38670.18131550.14742826X-RAY DIFFRACTION97

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