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- PDB-5gsc: Crystal structure of a class C beta lactamase of Apo form -

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Basic information

Entry
Database: PDB / ID: 5gsc
TitleCrystal structure of a class C beta lactamase of Apo form
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class C beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / nucleotide binding / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacter aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsAn, Y.J. / Cha, S.S.
CitationJournal: To Be Published
Title: Crystal structure of a class C beta lactamase of Apo form
Authors: Kim, M.K. / An, Y.J. / Na, J.H. / Cha, S.S.
History
DepositionAug 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,30526
Polymers78,6072
Non-polymers2,69824
Water4,828268
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,99016
Polymers39,3031
Non-polymers1,68615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,31510
Polymers39,3031
Non-polymers1,0129
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.511, 90.200, 113.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 39303.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: blaCMY-10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99QC1, beta-lactamase
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: 0.1M Cadmium chloride, 0.1M Na-Cacodylate pH4.6, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 53385 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 58.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZKU

1zku


Resolution: 1.953→48.161 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2707 5.07 %
Rwork0.1841 --
obs0.1862 53366 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.953→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 24 268 5585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085420
X-RAY DIFFRACTIONf_angle_d1.117359
X-RAY DIFFRACTIONf_dihedral_angle_d13.6061961
X-RAY DIFFRACTIONf_chiral_restr0.044805
X-RAY DIFFRACTIONf_plane_restr0.006959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9534-1.98890.26991430.18812462X-RAY DIFFRACTION92
1.9889-2.02710.27231300.19182669X-RAY DIFFRACTION100
2.0271-2.06850.24471250.19082665X-RAY DIFFRACTION99
2.0685-2.11350.24451460.18692670X-RAY DIFFRACTION100
2.1135-2.16270.24431420.18572659X-RAY DIFFRACTION100
2.1627-2.21670.25411540.18742663X-RAY DIFFRACTION100
2.2167-2.27670.2681340.23492472X-RAY DIFFRACTION92
2.2767-2.34370.22961490.18972669X-RAY DIFFRACTION99
2.3437-2.41930.2311390.19122666X-RAY DIFFRACTION100
2.4193-2.50580.23291430.18732698X-RAY DIFFRACTION100
2.5058-2.60610.22161600.18452656X-RAY DIFFRACTION100
2.6061-2.72470.2451500.20032686X-RAY DIFFRACTION100
2.7247-2.86830.24151310.19122708X-RAY DIFFRACTION100
2.8683-3.0480.23641450.2092710X-RAY DIFFRACTION100
3.048-3.28330.22531480.20522709X-RAY DIFFRACTION100
3.2833-3.61360.24531340.1912723X-RAY DIFFRACTION99
3.6136-4.13630.18691500.16342645X-RAY DIFFRACTION97
4.1363-5.21030.15481430.13182782X-RAY DIFFRACTION100
5.2103-48.17570.18791410.16692747X-RAY DIFFRACTION95

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