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- PDB-1nx4: The crystal structure of carbapenem synthase (CarC) -

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Basic information

Entry
Database: PDB / ID: 1nx4
TitleThe crystal structure of carbapenem synthase (CarC)
ComponentsCarbapenem synthase
KeywordsUNKNOWN FUNCTION / jelly roll
Function / homology
Function and homology information


(5R)-carbapenem-3-carboxylate synthase / dioxygenase activity / antibiotic biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / (5R)-carbapenem-3-carboxylate synthase
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsClifton, I.J. / Doan, L.X. / Sleeman, M.C. / Topf, M. / Suzuki, H. / Wilmouth, R.C. / Schofield, C.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of carbapenem synthase (CarC).
Authors: Clifton, I.J. / Doan, L.X. / Sleeman, M.C. / Topf, M. / Suzuki, H. / Wilmouth, R.C. / Schofield, C.J.
#1: Journal: J.CHEM.SOC.,CHEM.COMMUN. / Year: 1989
Title: A Chiral Synthesis of trans-Carbapenam-3-carboxylic Acid and the Assignment of (3S, 5S) Configuration to the Corresponding Product from Serratia and Erwinia Species.
Authors: Bycroft, B.W. / Chhabra, S.R.
#2: Journal: J.AM.CHEM.SOC. / Year: 2000
Title: Three Unusual Reactions Mediate Carbapenem and Carbapenam Biosynthesis
Authors: Li, R. / Stapon, A. / Blanchfield, J.T. / Townsend, C.A.
#3: Journal: MOL.MICROBIOL. / Year: 1997
Title: Analysis of the carbapenem gene cluster of Erwinia carotovora: definition of the antibiotic biosynthetic genes and evidence for a novel beta-lactam resistance mechanism
Authors: McGowan, S.J. / Sebaihia, M. / O'Leary, S. / Hardie, K.R. / Williams, P. / Stewart, G.S.A.B. / Bycroft, B.W. / Salmond, G.P.C.
#4: Journal: Trends Microbiol. / Year: 1998
Title: Bacterial production of carbapenems and clavams: evolution of beta-lactam antibiotic pathways
Authors: McGowan, S.J. / Bycroft, B.W. / Salmond, G.P.C.
#5: Journal: TETRAHEDRON LETT. / Year: 2002
Title: Diastereoselective synthesis of 3,5-trans-(+)-(3R,5R)-3- carbomethoxycarbapenam from 3-hydroxypyridine: questioning the stereochemical assignment of the natural product
Authors: Tanaka, H. / Sakagami, H. / Ogasawara, K.
History
DepositionFeb 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.end_auth_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

Downloads & links

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Assembly

Deposited unit
A: Carbapenem synthase
B: Carbapenem synthase
C: Carbapenem synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4009
Polymers95,7943
Non-polymers6066
Water4,378243
1
A: Carbapenem synthase
B: Carbapenem synthase
C: Carbapenem synthase
hetero molecules

A: Carbapenem synthase
B: Carbapenem synthase
C: Carbapenem synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,79918
Polymers191,5876
Non-polymers1,21212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)79.930, 163.946, 146.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA2 - 662 - 66
21SERSERGLUGLUBB2 - 662 - 66
31SERSERGLUGLUCC2 - 662 - 66
42THRTHRGLYGLYAA81 - 10481 - 104
52THRTHRGLYGLYBB81 - 10481 - 104
62THRTHRGLYGLYCC81 - 10481 - 104
73SERSERLEULEUAA109 - 160109 - 160
83SERSERLEULEUBB109 - 160109 - 160
93SERSERLEULEUCC109 - 160109 - 160
104TRPTRPASPASPAA173 - 272173 - 272
114TRPTRPASPASPBB173 - 272173 - 272
124TRPTRPASPASPCC173 - 272173 - 272
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operation: -x, y, 1/2-z

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Components

#1: Protein Carbapenem synthase / CarC


Mass: 31931.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: CarC / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9XB59
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, ammonium acetate, isopropanol, Tris, iron sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 mg/mlCarC1drop
210 mM2OG1drop
35 mM1dropFeSO4
44 %(w/v)PEG80001reservoir
5400 mM1reservoirNH4Ac
610 %(w/v)i-PrOH1reservoir
7100 mMTris-HCl1reservoirpH8.5
85 mM1reservoirFeSO4
910 mMdipotassium 2OG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9785, 0.9790, 1.0000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.9791
311
ReflectionResolution: 2.4→81.65 Å / Num. all: 173615 / Num. obs: 37852 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. measured all: 173615
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 99.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→81.65 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.596 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.418 / ESU R Free: 0.275
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1896 5 %RANDOM
Rwork0.22083 ---
all0.22317 37852 --
obs0.22317 35985 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.398 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2--0.98 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 33 243 6348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9358453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0293744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.741151034
X-RAY DIFFRACTIONr_chiral_restr0.1290.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024877
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1290.32699
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5979
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.51
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.335
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.53725
X-RAY DIFFRACTIONr_mcangle_it1.53325967
X-RAY DIFFRACTIONr_scbond_it2.4432522
X-RAY DIFFRACTIONr_scangle_it3.6694.52486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A35tight positional0.040.05
2B35tight positional0.050.05
3C35tight positional0.030.05
1A1887loose positional0.255
2B1887loose positional0.255
3C1887loose positional0.25
1A35tight thermal0.220.5
2B35tight thermal0.30.5
3C35tight thermal0.150.5
1A1887loose thermal1.8410
2B1887loose thermal2.1110
3C1887loose thermal1.9810
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.333 147
Rwork0.248 2634
obs-2781
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)
10.44040.1992-0.07311.80590.37322.09220.04360.072-0.0216-0.22910.087-0.2945-0.13340.5068-0.13060.1244-0.03080.12170.2281-0.04450.120119.32963.74316.592
20.61360.08280.30581.45370.20351.6491-0.0160.03330.0871-0.00670.1018-0.1771-0.30890.2516-0.08580.1927-0.08510.01530.092-0.03560.077814.52776.02453.978
30.9789-0.01880.21571.2786-0.06051.99870.19040.002-0.11080.0358-0.0392-0.19960.37270.2832-0.15130.18310.1181-0.11430.1007-0.04640.141915.57837.23245.771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 662 - 66
2X-RAY DIFFRACTION1AA81 - 10481 - 104
3X-RAY DIFFRACTION1AA109 - 160109 - 160
4X-RAY DIFFRACTION1AA173 - 272173 - 272
5X-RAY DIFFRACTION2BB2 - 662 - 66
6X-RAY DIFFRACTION2BB81 - 10481 - 104
7X-RAY DIFFRACTION2BB109 - 160109 - 160
8X-RAY DIFFRACTION2BB173 - 272173 - 272
9X-RAY DIFFRACTION3CC2 - 662 - 66
10X-RAY DIFFRACTION3CC81 - 10481 - 104
11X-RAY DIFFRACTION3CC109 - 160109 - 160
12X-RAY DIFFRACTION3CC173 - 272173 - 272
Refinement
*PLUS
Rfactor Rfree: 0.268 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.887

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