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- PDB-1m2x: Crystal Structure of the metallo-beta-lactamase BlaB of Chryseoba... -

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Basic information

Entry
Database: PDB / ID: 1m2x
TitleCrystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril
Componentsclass B carbapenemase BlaB-1
KeywordsHYDROLASE / ALPHA-BETA/BETA-ALPHA FOLD.
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MCO / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGarcia-Saez, I. / Dideberg, O.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The 1.5 A structure of Chryseobacterium meningosepticum Zn-beta-lactamase in complex with the inhibitor, D-captopril
Authors: Garcia-Saez, I. / Hopkins, J. / Papamicael, C. / Franceschini, N. / Amicosante, G. / Rossolini, G.M. / Galleni, M. / Frere, J.M. / Dideberg, O.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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

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Assembly

Deposited unit
A: class B carbapenemase BlaB-1
B: class B carbapenemase BlaB-1
C: class B carbapenemase BlaB-1
D: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53525
Polymers101,4904
Non-polymers2,04521
Water12,953719
1
A: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9017
Polymers25,3731
Non-polymers5296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: class B carbapenemase BlaB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8786
Polymers25,3731
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.685, 159.685, 97.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
class B carbapenemase BlaB-1 / metallo-beta-lactamase BlaB


Mass: 25372.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: blaB / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: O08498, beta-lactamase

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Non-polymers , 5 types, 740 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15NO3S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 28% PEG 4K, 0.2M Na Acetate, 0.1M Tris/Hcl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMsodium cacodylate1drop
3100000 mMzinc acetate1drop
4100000 mMdithiothreitol1droppH6.5
528 %PEG40001reservoir
60.2 Msodium acetate1reservoir
70.1 MTris-HCl1reservoirpH8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 138708 / Num. obs: 138708 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 13.189 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.117 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.2 / Num. unique all: 15550 / Rsym value: 0.177 / % possible all: 91.8
Reflection
*PLUS
Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVT

1bvt


Resolution: 1.5→10 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal showed cubic pseudo-symmetry. It belongs to the space group R3. NCS operators were not used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 12032 -random
Rwork0.19 ---
obs-133860 90 %-
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 93 719 7846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.5-1.510.2352520.2151X-RAY DIFFRACTION25254
1.97-20.21512400.1887X-RAY DIFFRACTION24034
2.41-2.480.19252380.1878X-RAY DIFFRACTION24564
4.39-5.530.20762150.1753X-RAY DIFFRACTION22734
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005

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