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- PDB-4dxb: 2.29A structure of the engineered MBP TEM-1 fusion protein RG13 i... -

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Basic information

Entry
Database: PDB / ID: 4dxb
Title2.29A structure of the engineered MBP TEM-1 fusion protein RG13 in complex with zinc, P1 space group
ComponentsMaltose-binding periplasmic protein, Beta-lactamase TEM chimera
KeywordsSUGAR BINDING PROTEIN / HYDROLASE / TEM / beta-lactamase / MBP / allosteric regulation / zinc binding / maltose binding
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / beta-lactam antibiotic catabolic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / beta-lactam antibiotic catabolic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / periplasmic space / response to antibiotic / DNA damage response / membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Periplasmic binding protein-like II / Beta-lactamase/transpeptidase-like / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
Authorsvan den Akker, F. / Ke, W.
CitationJournal: Plos One / Year: 2012
Title: Structure of an Engineered beta-Lactamase Maltose Binding Protein Fusion Protein: Insights into Heterotropic Allosteric Regulation.
Authors: Ke, W. / Laurent, A.H. / Armstrong, M.D. / Chen, Y. / Smith, W.E. / Liang, J. / Wright, C.M. / Ostermeier, M. / van den Akker, F.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / 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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: Maltose-binding periplasmic protein, Beta-lactamase TEM chimera
B: Maltose-binding periplasmic protein, Beta-lactamase TEM chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1366
Polymers139,8752
Non-polymers2624
Water8,827490
1
A: Maltose-binding periplasmic protein, Beta-lactamase TEM chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0683
Polymers69,9371
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, Beta-lactamase TEM chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0683
Polymers69,9371
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.316, 74.177, 103.130
Angle α, β, γ (deg.)83.54, 77.64, 89.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Maltose-binding periplasmic protein, Beta-lactamase TEM chimera / RG13


Mass: 69937.273 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, bla / Production host: Escherichia coli (E. coli) / Strain (production host): malE- auxotroph PM9F'
References: UniProt: P0AEX9, UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRG13 IS A CHIMERA COMPRISING THE N-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP ...RG13 IS A CHIMERA COMPRISING THE N-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 27-342), THE C-TERMINAL DOMAIN OF BETA-LACTAMASE TEM (UNP RESIDUES 227-286), AN ENGINEERED LINKER (GSGGG), THE N-TERMINAL DOMAIN OF BETA-LACTAMASE TEM (UNP RESIDUES 24-226), AN ENGINEERED LINKER (S), AND THE C-TERMINAL DOMAIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 345-396).

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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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) ...Details: A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) and equilibrated over a 1 ml reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2007 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0811
21.0811
ReflectionResolution: 2.29→31.45 Å / Num. all: 62117 / Num. obs: 59138 / % possible obs: 56.8 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5876 / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ZG4 AND 1OMP

1zg4

1omp


Resolution: 2.29→31.45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.733 / SU ML: 0.22 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29166 3008 5.1 %RANDOM
Rwork0.23183 ---
obs0.23492 56130 95.2 %-
all-59138 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2---0.01 Å20.01 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.29→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9834 0 4 490 10328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210064
X-RAY DIFFRACTIONr_angle_refined_deg0.961.96913652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.51551277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97125.046436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.174151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7091548
X-RAY DIFFRACTIONr_chiral_restr0.0620.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027608
X-RAY DIFFRACTIONr_nbd_refined0.1720.24906
X-RAY DIFFRACTIONr_nbtor_refined0.2930.26965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2563
X-RAY DIFFRACTIONr_metal_ion_refined0.070.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it1.60526524
X-RAY DIFFRACTIONr_mcangle_it2.551310160
X-RAY DIFFRACTIONr_scbond_it1.50524059
X-RAY DIFFRACTIONr_scangle_it2.25333489
LS refinement shellResolution: 2.29→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 201 -
Rwork0.264 3659 -
obs--85.78 %

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