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- PDB-5mmd: TMB-1. Structural insights into TMB-1 and the role of residue 119... -

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Basic information

Entry
Database: PDB / ID: 5mmd
TitleTMB-1. Structural insights into TMB-1 and the role of residue 119 and 228 in substrate and inhibitor binding
ComponentsMetallo-beta-lactamase 1
KeywordsHYDROLASE / Metallo-beta-lactamase / TMB-1 / TMB-2 / Thermal stability / enzyme kinetics / mutants
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase 1
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsSkagseth, S. / Christopeit, T. / Akhter, S. / Bayer, A. / Samuelsen, O. / Leiros, H.-K.S.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway213808 Norway
research Council of Norway SYNKNOYT 2011218539 Norway
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding.
Authors: Skagseth, S. / Christopeit, T. / Akhter, S. / Bayer, A. / Leiros, H.S.
History
DepositionDec 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.title
Revision 1.3Apr 25, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 2.0May 8, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Metallo-beta-lactamase 1
F: Metallo-beta-lactamase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7889
Polymers50,3912
Non-polymers3987
Water8,071448
1
E: Metallo-beta-lactamase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4626
Polymers25,1951
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Metallo-beta-lactamase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3263
Polymers25,1951
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.398, 127.195, 44.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-594-

HOH

21E-597-

HOH

31E-726-

HOH

41E-739-

HOH

51E-744-

HOH

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Components

#1: Protein Metallo-beta-lactamase 1


Mass: 25195.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaTMB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: T2HNV0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.10 M HEPES pH 8.0, 4.75% glycerol 32% polyethylene glycol (PEG) monomethyl ether (MME) 2k.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.75→48 Å / Num. obs: 38067 / % possible obs: 91.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.09 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4925 / Mean I/σ(I) obs: 1.7 / % possible all: 59.25

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.75→24.287 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97
RfactorNum. reflection% reflection
Rfree0.2479 1827 4.81 %
Rwork0.1924 --
obs0.1951 38019 91.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→24.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 7 448 3865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123500
X-RAY DIFFRACTIONf_angle_d1.3194730
X-RAY DIFFRACTIONf_dihedral_angle_d13.2241269
X-RAY DIFFRACTIONf_chiral_restr0.049512
X-RAY DIFFRACTIONf_plane_restr0.007598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79730.3981850.34471726X-RAY DIFFRACTION58
1.7973-1.85020.3739870.31892006X-RAY DIFFRACTION67
1.8502-1.90990.30861160.28462366X-RAY DIFFRACTION79
1.9099-1.97810.27821550.25152783X-RAY DIFFRACTION93
1.9781-2.05730.26831470.22932963X-RAY DIFFRACTION98
2.0573-2.15080.25481530.21442970X-RAY DIFFRACTION99
2.1508-2.26420.24751550.20432951X-RAY DIFFRACTION99
2.2642-2.40590.23131350.19133019X-RAY DIFFRACTION99
2.4059-2.59150.28191730.1863004X-RAY DIFFRACTION99
2.5915-2.85190.25681460.18343019X-RAY DIFFRACTION99
2.8519-3.26370.23441470.16783061X-RAY DIFFRACTION99
3.2637-4.10870.20981410.14833104X-RAY DIFFRACTION100
4.1087-24.28960.2261870.17343220X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.79270.231-0.01863.982-0.25583.9411-0.1410.08330.6008-0.08610.01270.5258-0.2361-0.39890.06660.12370.05570.01320.1447-0.00230.2198-23.95646.35374.8104
23.15440.50710.023.0372-0.36552.6332-0.0077-0.35690.0577-0.1453-0.0060.60580.0369-0.5531-0.01860.0586-0.00030.0010.20080.00580.2559-28.3843-2.64977.4426
32.20080.7413-0.28353.2417-0.94432.3031-0.11360.12410.0882-0.30480.0078-0.30280.0177-0.00560.07560.08330.00890.01330.093-0.02160.1733-16.8833-0.86363.8568
42.2708-0.23410.60012.45820.2372.0144-0.18760.2347-0.527-0.3174-0.0749-0.72670.19440.26660.17390.1340.00520.08970.1407-0.06040.3608-11.713-12.75975.6531
52.13960.41470.10221.93810.58881.7623-0.09080.2304-0.6340.10490.1202-0.60080.3770.45040.0980.19010.04360.05790.2254-0.01080.3575-9.8723-14.592810.0861
62.88570.5676-0.51722.384-0.55892.3293-0.0147-0.30140.13730.2362-0.0458-0.1967-0.03450.10280.06070.0970.0125-0.03950.1191-0.02780.154-17.7271-2.095221.3615
72.95490.5357-0.35728.3308-2.98174.08880.1046-0.45470.18530.7777-0.02650.302-0.2814-0.1519-0.09430.1490.02870.02140.2593-0.08480.1676-27.0331-2.821330.1693
82.4460.3016-0.10144.52921.42122.4883-0.0009-0.0745-0.06640.10920.0976-0.5446-0.16280.177-0.09310.16960.009-0.00570.11520.00510.2435-27.4431-33.53735.268
90.67120.4306-0.35391.6599-1.06575.55570.1021-0.0813-0.05470.45890.07950.3142-0.8783-0.5846-0.12010.31790.11750.06890.21450.04220.3239-36.5516-33.877612.4931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 38 through 51 )
2X-RAY DIFFRACTION2chain 'E' and (resid 52 through 64 )
3X-RAY DIFFRACTION3chain 'E' and (resid 65 through 124 )
4X-RAY DIFFRACTION4chain 'E' and (resid 125 through 148 )
5X-RAY DIFFRACTION5chain 'E' and (resid 149 through 175 )
6X-RAY DIFFRACTION6chain 'E' and (resid 179 through 279 )
7X-RAY DIFFRACTION7chain 'E' and (resid 280 through 297 )
8X-RAY DIFFRACTION8chain 'F' and (resid 39 through 88 )
9X-RAY DIFFRACTION9chain 'F' and (resid 89 through 295 )

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