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- PDB-1bul: 6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAM... -

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Basic information

Entry
Database: PDB / ID: 1bul
Title6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAMASE FROM ENTEROBACTER CLOACAE
ComponentsNMC-A BETA-LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CARBAPENEMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AP3 / Imipenem-hydrolyzing beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMourey, L. / Swaren, P. / Miyashita, K. / Bulychev, A. / Mobashery, S. / Samama, J.P.
CitationJournal: J.Am.Chem.Soc. / Year: 1998
Title: Inhibition of the Nmc-A B-Lactamase by a Penicillanic Acid Derivative, and the Structural Bases for the Increase in Substrate Profile of This Antibiotic Resistance Enzyme
Authors: Mourey, L. / Swaren, P. / Miyashita, K. / Bulychev, A. / Mobashery, S. / Samama, J.P.
History
DepositionSep 4, 1998Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NMC-A BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0015
Polymers29,1381
Non-polymers8634
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.550, 52.460, 67.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NMC-A BETA-LACTAMASE


Mass: 29137.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACYL-ENZYME COMPLEX / Source: (natural) Enterobacter cloacae (bacteria) / Strain: NOR-1 / References: UniProt: P52663, beta-lactamase
#2: Chemical ChemComp-AP3 / 2-(1-CARBOXY-2-HYDROXY-2-METHYL-PROPYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID


Mass: 277.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO5S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX BETWEEN 6 ALPHA-(HYDROXYPROPYL)PENICILLANIC ACID ...THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX BETWEEN 6 ALPHA-(HYDROXYPROPYL)PENICILLANIC ACID AND THE NMC-A BETA-LACTAMASE FROM ENTEROBACTER CLOACAE NOR-1. THE ACYLATED RESIDUE IS SER 70.
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: 2.35 Å3/Da / Density % sol: 47.2 %
Crystal growpH: 7.5
Details: 20% (W/V)PEG 1500, 0.200 M MES PH 5.25, 6% (V/V) N-PROPANOL, pH 7.5
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.89→18.6 Å / Num. obs: 22025 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 5.9 / % possible all: 95
Reflection
*PLUS
Num. measured all: 81088
Reflection shell
*PLUS
% possible obs: 95 % / Num. unique obs: 2019 / Num. measured obs: 6594

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE NMC-A BETA-LACTAMASE STRUCTURE

Resolution: 1.89→18.6 Å / Rfactor Rfree error: 0.0064 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT CORRECTION USED WITH A DENSITY OF 0.33 E-/A**3, SOLVENT RADIUS OF 0.25 ANGSTROMS AND B VALUES OF 50 A**2.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1625 7.3 %RANDOM
Rwork0.209 ---
obs0.209 22005 98.2 %-
Displacement parametersBiso mean: 13.1 Å2
Refine analyzeLuzzati d res low obs: 18.6 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.89→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 53 191 2292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.89→1.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 182 6.6 %
Rwork0.317 2458 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2MES.PARMES.TOP
X-RAY DIFFRACTION3PROPYL.PARPROPYL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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