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- PDB-1q19: Carbapenam Synthetase -

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Basic information

Entry
Database: PDB / ID: 1q19
TitleCarbapenam Synthetase
ComponentsCarA
KeywordsBIOSYNTHETIC PROTEIN / CMPr / (2S / 5S)-5-carboxymethylproline / b-LS / b-lactam synthetase / AS-B / class B asparagine synthetase / AMP-CPP / a / b-methyleneadenosine 5-triphosphate / CEA / N2-(carboxyethyl)-L-arginine / CMA / N2-(carboxylmethyl)-L-arginine
Function / homology
Function and homology information


carbapenam-3-carboxylate synthase / asparagine synthase (glutamine-hydrolyzing) activity / : / antibiotic biosynthetic process / ATP binding / cytosol
Similarity search - Function
Carbapenam-3-carboxylate synthase, N-terminal / Carbapenam-3-carboxylate synthase, N-terminal / : / Asparagine synthase / Asparagine synthase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold ...Carbapenam-3-carboxylate synthase, N-terminal / Carbapenam-3-carboxylate synthase, N-terminal / : / Asparagine synthase / Asparagine synthase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / (2S,5S)-5-CARBOXYMETHYLPROLINE / Carbapenam-3-carboxylate synthase
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMiller, M.T. / Gerratana, B. / Stapon, A. / Townsend, C.A. / Rosenzweig, A.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Carbapenam Synthetase (CarA)
Authors: Miller, M.T. / Gerratana, B. / Stapon, A. / Townsend, C.A. / Rosenzweig, A.C.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CarA
B: CarA
C: CarA
D: CarA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,02716
Polymers224,2164
Non-polymers2,81112
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-115 kcal/mol
Surface area68860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.042, 61.951, 175.870
Angle α, β, γ (deg.)90.00, 97.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CarA


Mass: 56054.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XB61
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-SSC / (2S,5S)-5-CARBOXYMETHYLPROLINE


Mass: 173.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H11NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 23-26 % (w/v) PEG 4000, 100 mM Na citrate, pH 5.6, 210-250 mM ammonium acetate, and 100 mM cesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris1droppH7.5
2100 mM1dropNaCl
30.4 ml/minprotein1drop
430 %(w/v)PEG33501reservoir
515 %(v/v)glycerol1reservoir
6100 mMsodium citrate1reservoirpH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.0024 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2002
RadiationMonochromator: Flat mirror (vertical focusing) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0024 Å / Relative weight: 1
ReflectionResolution: 2.3→49.83 Å / Num. all: 97443 / Num. obs: 86087 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.9 Å2 / Limit h max: 44 / Limit h min: -44 / Limit k max: 26 / Limit k min: -44 / Limit l max: 76 / Limit l min: 0 / Observed criterion F min: 6.9 / Rsym value: 0.084 / Net I/σ(I): 7.9
Reflection shellResolution: 2.4→2.53 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.368 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Num. obs: 86108 / Num. measured all: 294337 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.368

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q15

1q15


Resolution: 2.4→49.83 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2286342.04 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 8627 10 %Random
Rwork0.22 ---
all0.22 86841 --
obs0.27 86087 99.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 33.9229 Å2 / ksol: 0.363148 e/Å3
Displacement parametersBiso max: 95.4 Å2 / Biso mean: 33.68 Å2 / Biso min: 6.77 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20.04 Å2
2---5.97 Å20 Å2
3---1.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15704 0 176 399 16279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_torsion_deg22.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.335110310.50.27394520.01107761055597.9
2.51-2.640.32810359.80.26495440.01107601057998.3
2.64-2.810.31110549.90.24896240.01108061067898.8
2.81-3.020.305110510.30.24796290.009107971073499.4
3.02-3.330.2910749.90.23697270.009108421080199.6
3.33-3.810.259110010.20.21897320.008108621083299.7
3.81-4.80.23710579.70.18198140.007109191087199.6
4.8-49.830.2451099100.20199380.007111471103799
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4lig.paramlig.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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