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- PDB-6v72: Crystal Structure of Metallo Beta Lactamase from Erythrobacter li... -

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Basic information

Entry
Database: PDB / ID: 6v72
TitleCrystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis
ComponentsBeta-lactamase II
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / 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
FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesErythrobacter litoralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMaltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,74712
Polymers26,2851
Non-polymers46211
Water3,585199
1
A: Beta-lactamase II
hetero molecules

A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49524
Polymers52,5702
Non-polymers92422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+21
Buried area3590 Å2
ΔGint-117 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.985, 96.985, 45.186
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-305-

CL

21A-403-

HOH

31A-547-

HOH

41A-594-

HOH

51A-599-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase II


Mass: 26285.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Erythrobacter litoralis (strain HTCC2594) (bacteria)
References: UniProt: Q2N9N3

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M CaCl2;0.1M TRIS pH 8.5; 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.5→33.06 Å / Num. obs: 39040 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.87 Å2 / Rsym value: 0.076 / Net I/σ(I): 24.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1817 / CC1/2: 0.571 / Rsym value: 0.719

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→33.06 Å / SU ML: 0.1724 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.5438
RfactorNum. reflection% reflection
Rfree0.1834 1929 4.94 %
Rwork0.1486 --
obs0.1504 39023 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 15 199 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861778
X-RAY DIFFRACTIONf_angle_d0.95312432
X-RAY DIFFRACTIONf_chiral_restr0.06274
X-RAY DIFFRACTIONf_plane_restr0.0063324
X-RAY DIFFRACTIONf_dihedral_angle_d23.3477250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.30061440.23652437X-RAY DIFFRACTION92.91
1.54-1.580.29571180.19352557X-RAY DIFFRACTION96.78
1.58-1.630.2321530.15452634X-RAY DIFFRACTION99.39
1.63-1.680.20261480.13022644X-RAY DIFFRACTION100
1.68-1.740.18251320.11682637X-RAY DIFFRACTION100
1.74-1.810.17741480.12552659X-RAY DIFFRACTION100
1.81-1.890.18611420.12192640X-RAY DIFFRACTION100
1.89-1.990.19041260.12952663X-RAY DIFFRACTION100
1.99-2.120.1881220.13382669X-RAY DIFFRACTION100
2.12-2.280.18711600.13822659X-RAY DIFFRACTION100
2.28-2.510.20161090.14332707X-RAY DIFFRACTION100
2.51-2.870.18981520.15582679X-RAY DIFFRACTION100
2.87-3.610.17091470.15672687X-RAY DIFFRACTION100
3.62-33.060.15121280.15872822X-RAY DIFFRACTION99.73

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