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- PDB-5e2f: Crystal Structure of Beta-lactamase class D from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5e2f
TitleCrystal Structure of Beta-lactamase class D from Bacillus subtilis
ComponentsBeta-lactamase YbxI
KeywordsHYDROLASE / beta lactamase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable beta-lactamase YbxI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsKim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Beta-lactamase class D from Bacillus subtilis
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,0578
Polymers62,7512
Non-polymers3066
Water9,368520
1
A: Beta-lactamase YbxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5805
Polymers31,3751
Non-polymers2044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase YbxI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4773
Polymers31,3751
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.699, 68.856, 153.979
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 YbxI


Mass: 31375.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: acylated lysine
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ybxI, ybdS, BSU02090 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 gold / References: UniProt: P54427, beta-lactamase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Calcium Chloride, 0.1 M Tris:HCl pH 8.5, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.3→28.112 Å / Num. obs: 123708 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.056 / Net I/σ(I): 20.22
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.67 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.10pre-2104refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→28.112 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 13.08 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1521 5731 4.87 %Random selection
Rwork0.125 ---
obs0.1263 117679 93.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→28.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 15 520 4415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094287
X-RAY DIFFRACTIONf_angle_d1.0815813
X-RAY DIFFRACTIONf_dihedral_angle_d19.6461630
X-RAY DIFFRACTIONf_chiral_restr0.09608
X-RAY DIFFRACTIONf_plane_restr0.008768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3002-1.31490.2526710.19481374X-RAY DIFFRACTION35
1.3149-1.33040.19811100.17992170X-RAY DIFFRACTION55
1.3304-1.34660.19321380.17182884X-RAY DIFFRACTION73
1.3466-1.36370.2361850.16843346X-RAY DIFFRACTION85
1.3637-1.38160.19692160.15683710X-RAY DIFFRACTION95
1.3816-1.40060.19761950.15993883X-RAY DIFFRACTION97
1.4006-1.42060.21321870.14243806X-RAY DIFFRACTION98
1.4206-1.44180.18681960.12583943X-RAY DIFFRACTION99
1.4418-1.46430.15352070.11773893X-RAY DIFFRACTION99
1.4643-1.48830.14892040.11163898X-RAY DIFFRACTION99
1.4883-1.5140.14391830.10363905X-RAY DIFFRACTION99
1.514-1.54150.15512180.10113911X-RAY DIFFRACTION99
1.5415-1.57110.12981970.10113955X-RAY DIFFRACTION100
1.5711-1.60320.14841960.09713908X-RAY DIFFRACTION99
1.6032-1.63810.15162160.0973926X-RAY DIFFRACTION99
1.6381-1.67620.13592260.09393880X-RAY DIFFRACTION99
1.6762-1.71810.14191940.09613905X-RAY DIFFRACTION99
1.7181-1.76450.15072000.10373938X-RAY DIFFRACTION99
1.7645-1.81640.14522290.10233895X-RAY DIFFRACTION99
1.8164-1.8750.12861930.10383932X-RAY DIFFRACTION99
1.875-1.9420.15731880.10683948X-RAY DIFFRACTION99
1.942-2.01980.13262080.10713925X-RAY DIFFRACTION99
2.0198-2.11170.13031970.10813949X-RAY DIFFRACTION99
2.1117-2.2230.15211840.12113974X-RAY DIFFRACTION99
2.223-2.36220.15081850.123998X-RAY DIFFRACTION99
2.3622-2.54440.1552050.13573989X-RAY DIFFRACTION99
2.5444-2.80030.16481910.14294016X-RAY DIFFRACTION99
2.8003-3.2050.17181990.14373982X-RAY DIFFRACTION99
3.205-4.03610.14021960.13484040X-RAY DIFFRACTION98
4.0361-28.11880.14752170.13754065X-RAY DIFFRACTION95

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