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- PDB-3x2z: Crystal structure of metallo-beta-lactamase in complex with nicke... -

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Basic information

Entry
Database: PDB / ID: 3x2z
TitleCrystal structure of metallo-beta-lactamase in complex with nickel from Thermotoga maritima
ComponentsUPF0173 metal-dependent hydrolase TM_1162
KeywordsHYDROLASE
Function / homology
Function and homology information


Protein of unknown funcion UPF0173 / : / Beta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / UPF0173 metal-dependent hydrolase TM_1162
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsChoi, H.J. / Kim, H.J. / Matsuura, A. / Mikami, B. / Yoon, H.J. / Lee, H.H.
CitationJournal: To be Published
Title: Crystal structure of metallo-beta-lactamase in complex with nickel from Thermotoga maritima
Authors: Choi, H.J. / Kim, H.J. / Matsuura, A. / Mikami, B. / Yoon, H.J. / Lee, H.H.
History
DepositionJan 7, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0173 metal-dependent hydrolase TM_1162
B: UPF0173 metal-dependent hydrolase TM_1162
C: UPF0173 metal-dependent hydrolase TM_1162
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5549
Polymers74,2013
Non-polymers3526
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-86 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.538, 143.538, 149.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UPF0173 metal-dependent hydrolase TM_1162


Mass: 24733.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_1162 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q9X0P5
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 5.2 Å3/Da / Density % sol: 76.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 55% 2-Methyl-2,4-pentanediol(MPD), pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2013
RadiationMonochromator: Si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 66863 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.33→2.37 Å / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 7.633 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→48.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.419 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20508 2009 3.1 %RANDOM
Rwork0.19073 ---
all0.19118 62672 --
obs0.19118 62672 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.565 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.33→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 6 323 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195316
X-RAY DIFFRACTIONr_bond_other_d0.0060.025244
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9757179
X-RAY DIFFRACTIONr_angle_other_deg0.665312144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5035678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82425.147204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23315948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.593159
X-RAY DIFFRACTIONr_chiral_restr0.050.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7913.3822721
X-RAY DIFFRACTIONr_mcbond_other0.7913.3812720
X-RAY DIFFRACTIONr_mcangle_it1.4565.0673396
X-RAY DIFFRACTIONr_mcangle_other1.4565.0683397
X-RAY DIFFRACTIONr_scbond_it0.6713.5152595
X-RAY DIFFRACTIONr_scbond_other0.6713.5152596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2455.2193784
X-RAY DIFFRACTIONr_long_range_B_refined3.22727.2486174
X-RAY DIFFRACTIONr_long_range_B_other2.98626.996042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.334→2.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 134 -
Rwork0.237 4344 -
obs--91.93 %

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