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- PDB-2jb8: Deacetoxycephalosporin C synthase complexed with 5-hydroxy-4-keto... -

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Basic information

Entry
Database: PDB / ID: 2jb8
TitleDeacetoxycephalosporin C synthase complexed with 5-hydroxy-4-keto valeric acid
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHETASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / MONONUCLEAR FERROUS ENZYME / IRON / VITAMIN C
Function / homology
Function and homology information


deacetoxycephalosporin-C synthase / deacetoxycephalosporin-C synthase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
: / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. ...: / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 4,5-DIOXOPENTANOIC ACID / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCicero, G. / Carbonera, C. / Valegard, K. / Hajdu, J. / Andersson, I. / Ranghino, G.
CitationJournal: Int.J.Quantum Chem. / Year: 2007
Title: Study of the Oxidative Half-Reaction Catalysed by a Non-Heme Ferrous Catalytic Centre by Means of Structural and Computational Methodologies
Authors: Cicero, G. / Carbonera, C. / Valegard, K. / Hajdu, J. / Andersson, I. / Ranghino, G.
History
DepositionDec 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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 / _struct_conn.pdbx_dist_value / _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_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: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7783
Polymers34,5921
Non-polymers1862
Water3,909217
1
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3339
Polymers103,7753
Non-polymers5586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7960 Å2
ΔGint-69.4 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.500, 106.500, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2091-

HOH

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHETASE / DAOCS / EXPANDASE / DEACETOXYCEPHALOSPORIN C SYNTHASE


Mass: 34591.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P18548, deacetoxycephalosporin-C synthase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HKV / 4,5-DIOXOPENTANOIC ACID


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.53→24.92 Å / Num. obs: 42610 / % possible obs: 93.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.29 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXF

1rxf


Resolution: 1.53→24.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.574 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1938 5 %RANDOM
Rwork0.21 ---
obs0.212 36752 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 10 217 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9552966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5035269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38422.642106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1721521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21000
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21525
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.51383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4622177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1963898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.274.5789
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
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 139
Rwork0.29 2573
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59940.06280.07220.40720.01090.1487-0.0108-0.04810.08220.0616-0.0334-0.032-0.0095-0.01110.04420.0055-0.0064-0.0102-0.0122-0.0052-0.02397.730121.851352.2699
20.6524-0.1224-0.02110.94920.1380.3665-0.0060.0520.0209-0.0224-0.0244-0.09850.0188-0.02710.03040.0003-0.00560.0035-0.00280.0042-0.02839.91923.955639.271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 260
2X-RAY DIFFRACTION2A270 - 309

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