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- PDB-1nx8: Structure of carbapenem synthase (CarC) complexed with N-acetyl p... -

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Basic information

Entry
Database: PDB / ID: 1nx8
TitleStructure of carbapenem synthase (CarC) complexed with N-acetyl proline
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 / : / 1-ACETYL-L-PROLINE / (5R)-carbapenem-3-carboxylate synthase
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 10, 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 1.3Jul 11, 2012Group: Non-polymer description
Revision 1.4Aug 17, 2016Group: Non-polymer description
Revision 2.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Carbapenem synthase
B: Carbapenem synthase
C: Carbapenem synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,87011
Polymers94,9503
Non-polymers9208
Water4,179232
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)191,73922
Polymers189,8996
Non-polymers1,84016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)80.443, 164.082, 146.330
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: 4

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
73SERSERVALVALAA109 - 159109 - 159
83SERSERVALVALBB109 - 159109 - 159
93SERSERVALVALCC109 - 159109 - 159
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: 31649.861 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: Chemical ChemComp-N7P / 1-ACETYL-L-PROLINE / N-ACETYLPROLINE


Type: L-peptide linking / Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.72 Å3/Da / Density % sol: 54.35 %
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: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→24.885 Å / Num. all: 157442 / Num. obs: 41629 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.2 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. obs: 41822 / Num. measured all: 157442
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 98.6 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NX4

1nx4


Resolution: 2.3→81.65 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.917 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.362 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 2082 5 %RANDOM
Rwork0.22751 ---
all0.22991 41629 --
obs0.22991 39546 95.99 %-
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: 22.561 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2--0.49 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 55 232 6350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216260
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9328468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.813741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.968151050
X-RAY DIFFRACTIONr_chiral_restr0.120.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024890
X-RAY DIFFRACTIONr_nbd_refined0.1150.32698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.5928
X-RAY DIFFRACTIONr_metal_ion_refined0.2050.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.520
X-RAY DIFFRACTIONr_mcbond_it0.5561.53710
X-RAY DIFFRACTIONr_mcangle_it0.98825947
X-RAY DIFFRACTIONr_scbond_it1.68632550
X-RAY DIFFRACTIONr_scangle_it2.6144.52521
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A50tight positional0.040.05
2B50tight positional0.040.05
3C50tight positional0.040.05
1A1864medium positional0.190.5
2B1864medium positional0.210.5
3C1864medium positional0.170.5
1A50tight thermal0.110.5
2B50tight thermal0.130.5
3C50tight thermal0.10.5
1A1864medium thermal0.672
2B1864medium thermal0.732
3C1864medium thermal0.652
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.34 157
Rwork0.284 2923
obs-3080
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)
10.9476-0.2997-0.92452.5124-0.13964.1470.08340.0813-0.0569-0.4407-0.00320.0260.11360.1381-0.08030.28030.01320.04980.1359-0.04540.02579.88957.5587.077
20.46260.2205-0.07721.64360.43332.12890.09530.02790.1006-0.18980.0928-0.3694-0.1580.6966-0.18810.2304-0.04970.14190.2889-0.06570.151323.00365.90618.151
30.5360.41130.1852.09930.33851.99410.06750.07660.0276-0.08270.0632-0.3273-0.17630.6205-0.13070.1816-0.05350.11220.2672-0.05430.093122.75166.4120.68
41.0756-0.13030.5041.59130.65563.8506-0.09910.13750.2415-0.12640.08280.0649-0.71340.02330.01630.4131-0.0320.01940.06320.00160.06934.51386.29651.384
50.395-0.15240.41321.42610.391.5036-0.01660.0480.05620.05620.17-0.2511-0.21610.3-0.15330.2317-0.08060.00860.1225-0.04120.079417.8875.38657.132
60.2193-0.06880.27781.8595-0.0141.868-0.0130.00690.05530.01020.1117-0.2737-0.190.3618-0.09870.2231-0.07150.00410.1168-0.05080.061718.29971.50754.958
71.5064-0.4450.66054.2721-1.17653.0520.2221-0.2437-0.09080.1639-0.06950.10130.4549-0.1207-0.15260.2988-0.0104-0.11090.10040.00250.06673.69133.41353.81
80.8576-0.2920.2321.3953-0.30041.56180.2140.0581-0.115-0.0645-0.0777-0.27470.44450.438-0.13640.26390.1485-0.08520.1639-0.04250.127519.62437.26244.103
90.7121-0.15280.06351.2928-0.06142.1560.18980.0794-0.1149-0.0115-0.055-0.24590.22060.4488-0.13480.2450.1471-0.09580.1728-0.05260.101319.89639.07642.174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 662 - 66
2X-RAY DIFFRACTION2AA79 - 16079 - 160
3X-RAY DIFFRACTION3AA173 - 272173 - 272
4X-RAY DIFFRACTION4BB2 - 672 - 67
5X-RAY DIFFRACTION5BB74 - 16074 - 160
6X-RAY DIFFRACTION6BB172 - 272172 - 272
7X-RAY DIFFRACTION7CC2 - 662 - 66
8X-RAY DIFFRACTION8CC80 - 16080 - 160
9X-RAY DIFFRACTION9CC173 - 272173 - 272
Refinement
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.725

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