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- PDB-1e5h: DELTA-R307A DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCC... -

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Basic information

Entry
Database: PDB / ID: 1e5h
TitleDELTA-R307A DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE AND CARBON DIOXIDE
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHASE
KeywordsOXIDOREDUCTASE / FERROUS OXYGENASE / CEPHALOSPORIN / 2-OXOGLUTARATE / C-TERMINUS ANTIBIOTICS / OXIDATIVE COUPLING CONTROL
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. / Jelly Rolls ...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
CARBON DIOXIDE / : / SUCCINIC ACID / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLee, H.J. / Lloyd, M.D. / Harlos, K. / Clifton, I.J. / Baldwin, J.E. / Schofield, C.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Kinetic and Crystallographic Studies on Deacetoxycephalosporin C Synthase (Daocs)
Authors: Lee, H.J. / Lloyd, M.D. / Harlos, K. / Clifton, I.J. / Baldwin, J.E. / Schofield, C.J.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Studies on the Active Site of Deacetoxycephalosporin C Synthase (Daocs)
Authors: Lloyd, M.D. / Lee, H.J. / Harlos, K. / Zhang, Z.-H. / Baldwin, J.E. / Schofield, C.J. / Charnock, J.M. / Garner, C.D. / Hara, T. / Terrwisscha Van Scheltinga, A.C. / Valegard, K. / Viklund, ...Authors: Lloyd, M.D. / Lee, H.J. / Harlos, K. / Zhang, Z.-H. / Baldwin, J.E. / Schofield, C.J. / Charnock, J.M. / Garner, C.D. / Hara, T. / Terrwisscha Van Scheltinga, A.C. / Valegard, K. / Viklund, J.A.C. / Hajdu, J. / Andersson, I. / Danielsson, A. / Bhikhabhai, R.
History
DepositionJul 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4924
Polymers34,2741
Non-polymers2183
Water2,144119
1
A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,47712
Polymers102,8233
Non-polymers6549
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 area8600 Å2
ΔGint-29.9 kcal/mol
Surface area37920 Å2
MethodPQS
Unit cell
Length a, b, c (Å)106.260, 106.260, 71.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsBIOLOGICALUNIT: ACTIVE AS A MONOMER, TRIMERIC ASSEMBLYOBSERVED IN THE CRYSTAL.

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHASE / RING EXPANDING ENZYME / RING EXPANDASE


Mass: 34274.277 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Description: RECOMBINANT E.COLI / Gene: CEFE / Plasmid: PET 24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18548
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION THR308ALA. THE C-TERMINAL RESIDUES SER, LYS, ALA ARE DELETED. FUNCTION: ...CHAIN A ENGINEERED MUTATION THR308ALA. THE C-TERMINAL RESIDUES SER, LYS, ALA ARE DELETED. FUNCTION: DAOCS CATALYZES THE STEP FROM PENICILLIN N TO DEACETOXY- CEPHALOSPORIN C. COFACTOR: IRON AND ASCORBATE. PATHWAY: BIOSYNTHESIS OF CEPHALOSPORIN ANTIBIOTICS. SIMILARITY: BELONGS TO THE IRONULLSCORBATE-DEPENDENT FAMILY OF OXIDOREDUCTASES. STRONG, TO CEFF.
Sequence detailsILE A 50, WRONGLY REPORTED IN DATABASE

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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: 2.39 Å3/Da / Density % sol: 48.16 %
Crystal growpH: 7
Details: 100 MM HEPES-NAOH, PH 7.0, 0.5 MM PB(OAC)2(OH2)2, 5 MM NA2SUCCINATE, 5 MM NAHCO3, GLYCEROL 5-10% (W/V), 1.4-1.6 M AMMONIUM SULPHATE
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Lloyd, M.D., (1999) J.Mol.Biol., 287, 943.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES-NaOH1reservoir
25 mMpotassium 2-oxoglutarate1reservoir
31.6-1.7 Mammonium sulfate1reservoir
455 mMHEPES-NaOH1drop
52.5 mMpotassium 2-oxoglutarate1drop
60.8-0.85 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 28, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 21766 / % possible obs: 99.8 % / Redundancy: 5.92 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.9
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 6.29 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 128961 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSRIGID BODY REFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RXF

1rxf


Resolution: 1.96→16.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2006850.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DATA DETWINNED USING CCP4 PROGRAMME DETWIN (A. LESLIE)
RfactorNum. reflection% reflectionSelection details
Rfree0.252 912 4.3 %RANDOM
Rwork0.22 ---
obs0.22 21428 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8877 Å2 / ksol: 0.392467 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20.75 Å20 Å2
2---1.39 Å20 Å2
3---2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.96→16.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 12 119 2257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 137 3.8 %
Rwork0.263 3454 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4SUCCINATE.PARSUCCINATE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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