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- PDB-4f6z: Mutagenesis of zinc ligand residue Cys221 reveals plasticity in t... -

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Basic information

Entry
Database: PDB / ID: 4f6z
TitleMutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-b-lactamase active site
ComponentsBeta-lactamase
KeywordsHYDROLASE / metallo-b-lactamase / b-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / 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
CITRATE ANION / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorton, L.B. / Shanker, S. / Sankaran, B. / Mikulski, R. / Brown, N.G. / Phillips, K. / Lykissa, E. / Prasad, B.V.V. / Palzkill, T.G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: Mutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-beta-lactamase active site
Authors: Horton, L.B. / Shanker, S. / Mikulski, R. / Brown, N.G. / Phillips, K.J. / Lykissa, E. / Venkataram Prasad, B.V. / Palzkill, T.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3973
Polymers26,1431
Non-polymers2552
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.031, 59.774, 83.552
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 / Beta-lactamase IMP-1 / Bla-imp protein / Extended-spectrum B-lactamase / IMP-1 metallo-beta- ...Beta-lactamase IMP-1 / Bla-imp protein / Extended-spectrum B-lactamase / IMP-1 metallo-beta-lactmase / Metallo beta lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase IMP-1 / Metallo-beta-lactamase blaIMP-1


Mass: 26142.732 Da / Num. of mol.: 1 / Mutation: C176G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaIMP-1, bla IMP, bla-imp, blaESP, imp / Production host: Escherichia coli (E. coli) / References: UniProt: Q79MP6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25 mMTris-HCl containing 1 mM zinc sulfate at pH 7.0, and 25 mMTris-HCl with 1 mM zinc chloride at pH 7.0, and the mother liquor which consisted of 0.1 M tri-sodium citrate (pH 5.5) in 40% ...Details: 25 mMTris-HCl containing 1 mM zinc sulfate at pH 7.0, and 25 mMTris-HCl with 1 mM zinc chloride at pH 7.0, and the mother liquor which consisted of 0.1 M tri-sodium citrate (pH 5.5) in 40% PEG 600., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25.24 Å / Num. all: 15635 / Num. obs: 15635 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.04 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.1 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4F6H

4f6h


Resolution: 2→25.24 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 794 5.09 %RANDOM
Rwork0.1988 ---
all0.2013 15635 --
obs0.2013 15601 89.2 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.42 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.605 Å20 Å2-0 Å2
2--8.0412 Å2-0 Å2
3----1.4362 Å2
Refinement stepCycle: LAST / Resolution: 2→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 14 151 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151856
X-RAY DIFFRACTIONf_angle_d1.0442431
X-RAY DIFFRACTIONf_dihedral_angle_d13.201648
X-RAY DIFFRACTIONf_chiral_restr0.066266
X-RAY DIFFRACTIONf_plane_restr0.005306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.28361490.24492485X-RAY DIFFRACTION93
2.1253-2.28930.26031310.21832513X-RAY DIFFRACTION92
2.2893-2.51950.29191380.21382481X-RAY DIFFRACTION91
2.5195-2.88360.33141300.2242470X-RAY DIFFRACTION90
2.8836-3.63130.21491330.18982433X-RAY DIFFRACTION88
3.6313-25.24690.22131130.17982425X-RAY DIFFRACTION83
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)
11.5627-0.12940.06051.14050.3110.7119-0.0296-0.27550.01910.33270.0449-0.3006-0.2101-0.15750.02440.2448-0.0346-0.02660.2693-0.03080.185624.659521.746517.9066
21.0344-0.05270.20690.3993-0.29850.6663-0.0342-0.1517-0.0789-0.0416-0.0586-0.21970.0740.10080.0230.18080.0003-0.01080.19420.03960.198724.561912.392512.6772
31.8030.10240.23590.68330.08610.6061-0.0319-0.0679-0.07420.0343-0.10150.01460.0657-0.10650.04650.1583-0.03030.01080.2027-0.00610.174412.766316.35057.7505
41.34620.05720.46750.36960.22720.283-0.0691-0.49690.5478-0.0095-0.25020.36-0.4231-0.6940.02240.30240.079-0.03770.4062-0.15660.33135.534928.714515.2525
50.6247-0.01810.17510.3950.06240.2869-0.12-0.14040.1671-0.049-0.03980.1182-0.0877-0.17930.17330.48350.1665-0.23580.7048-0.27260.572320.381541.601314.5888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:40)
2X-RAY DIFFRACTION2chain 'A' and (resseq 41:85)
3X-RAY DIFFRACTION3chain 'A' and (resseq 86:172)
4X-RAY DIFFRACTION4chain 'A' and (resseq 173:220)
5X-RAY DIFFRACTION5chain 'A' and (resseq 231:236)

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