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- PDB-4cfs: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Entry
Database: PDB / ID: 4cfs
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE
Components1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE COMPLEX / DIOXYGENASE / COFACTOR-DEVOID
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function
Uteroglobin - #20 / Uteroglobin / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Uteroglobin - #20 / Uteroglobin / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE / : / D(-)-TARTARIC ACID / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesARTHROBACTER NITROGUAJACOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.94 Å
AuthorsBui, S. / Steiner, R.A.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Origin of the Proton-Transfer Step in the Cofactor-Free 1-H-3-Hydroxy-4-Oxoquinaldine 2,4- Dioxygenase: Effect of the Basicity of an Active Site His Residue.
Authors: Hernandez-Ortega, A. / Quesne, M.G. / Bui, S. / Heuts, D.P. / Steiner, R.A. / Heyes, D.J. / De Visser, S.P. / Scrutton, N.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the Alpha/Beta-Hydrolase Fold.
Authors: Steiner, R.A. / Janssen, H.J. / Roversi, P. / Oakley, A.J. / Fetzner, S.
History
DepositionNov 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
B: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
C: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
D: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,33719
Polymers132,4294
Non-polymers1,90815
Water11,494638
1
A: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4724
Polymers33,1071
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3213
Polymers33,1071
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7726
Polymers33,1071
Non-polymers6655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7726
Polymers33,1071
Non-polymers6655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.730, 166.850, 167.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLYAA3 - 27514 - 286
21ASPASPGLYGLYBB3 - 27514 - 286
12ASPASPGLYGLYAA3 - 27514 - 286
22ASPASPGLYGLYCC3 - 27514 - 286
13THRTHRGLNGLNAA4 - 27415 - 285
23THRTHRGLNGLNDD4 - 27415 - 285
14ASPASPGLYGLYBB3 - 27514 - 286
24ASPASPGLYGLYCC3 - 27514 - 286
15THRTHRGLNGLNBB4 - 27415 - 285
25THRTHRGLNGLNDD4 - 27415 - 285
16THRTHRGLNGLNCC4 - 27415 - 285
26THRTHRGLNGLNDD4 - 27415 - 285

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE


Mass: 33107.195 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER NITROGUAJACOLICUS (bacteria)
Strain: RU61A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HQD / 3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE


Mass: 175.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO2
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMRGSHHHHHHGS N-TERMINAL PURIFICATION TAG C69S, ENGINEERED MUTATION H251A, ENGINEERED MUTATION

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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: 2.56 Å3/Da / Density % sol: 51.96 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 5, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.511
11-H, L, K20.489
ReflectionResolution: 1.95→46.45 Å / Num. obs: 92811 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 7.73 % / Biso Wilson estimate: 24.648 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.84 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.94→46.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.588 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TNCS IS PRESENT FRAC 0.000 0.407 0.407
RfactorNum. reflection% reflectionSelection details
Rfree0.19841 4709 5.1 %THIN SHELLS TAKING TWIN LAW INTO CONSIDERATION
Rwork0.16287 ---
obs0.16464 88008 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.945 Å2
Baniso -1Baniso -2Baniso -3
1--6.94 Å20 Å20 Å2
2--3.29 Å20 Å2
3---3.65 Å2
Refinement stepCycle: LAST / Resolution: 1.94→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8880 0 126 638 9644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199427
X-RAY DIFFRACTIONr_bond_other_d0.0040.028598
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.94812860
X-RAY DIFFRACTIONr_angle_other_deg0.917319817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82851127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01923.483491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.312151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1441574
X-RAY DIFFRACTIONr_chiral_restr0.0740.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111022
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022292
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_it1.7922.8844406
X-RAY DIFFRACTIONr_mcbond_other1.7912.8844407
X-RAY DIFFRACTIONr_mcangle_it2.6664.3125517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.993.0625021
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A174530.05
12B174530.05
21A175410.05
22C175410.05
31A174340.05
32D174340.05
41B175750.04
42C175750.04
51B174400.05
52D174400.05
61C174920.05
62D174920.05
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 238 -
Rwork0.201 5341 -
obs--81.98 %

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