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- PDB-6knt: Crystal structure of the metallo-beta-lactamase fold protein YhfI... -

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Basic information

Entry
Database: PDB / ID: 6knt
TitleCrystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group P4332)
ComponentsPutative metal-dependent hydrolase
KeywordsHYDROLASE / enzyme / metallo-beta-lactamase fold protein
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / metal ion binding
Similarity search - Function
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
Putative metal-dependent hydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNa, H.W. / Namgung, B. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural and biochemical analyses of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis.
Authors: Na, H.W. / Namgung, B. / Song, W.S. / Yoon, S.I.
History
DepositionAug 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Putative metal-dependent hydrolase
B: Putative metal-dependent hydrolase
C: Putative metal-dependent hydrolase
D: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,84912
Polymers108,3254
Non-polymers5238
Water2,540141
1
A: Putative metal-dependent hydrolase
B: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4246
Polymers54,1632
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-176 kcal/mol
Surface area18120 Å2
MethodPISA
2
C: Putative metal-dependent hydrolase
D: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4246
Polymers54,1632
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-178 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.754, 202.754, 202.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 290
2115B1 - 290
3115C1 - 290
4115D1 - 290

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Components

#1: Protein
Putative metal-dependent hydrolase


Mass: 27081.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhfI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E0TYN8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfate, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 49583 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 30.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4859 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 6KNS

6kns


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.774 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.328 / ESU R Free: 0.234 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 2497 5.1 %RANDOM
Rwork0.1901 ---
obs0.192 46839 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 122.28 Å2 / Biso mean: 44.73 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7426 0 8 141 7575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217628
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.93810379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63424.551334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.199151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2721512
X-RAY DIFFRACTIONr_chiral_restr0.0870.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215894
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A972MEDIUM POSITIONAL0.130.5
2B972MEDIUM POSITIONAL0.140.5
3C972MEDIUM POSITIONAL0.150.5
4D972MEDIUM POSITIONAL0.130.5
1A839LOOSE POSITIONAL0.295
2B839LOOSE POSITIONAL0.295
3C839LOOSE POSITIONAL0.315
4D839LOOSE POSITIONAL0.285
1A972MEDIUM THERMAL0.562
2B972MEDIUM THERMAL0.542
3C972MEDIUM THERMAL0.482
4D972MEDIUM THERMAL0.512
1A839LOOSE THERMAL0.8410
2B839LOOSE THERMAL0.7210
3C839LOOSE THERMAL0.6710
4D839LOOSE THERMAL0.6910
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 190 -
Rwork0.298 3370 -
all-3560 -
obs--99.5 %
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)
11.7821-0.06630.39591.80540.05521.1940.00330.0770.0202-0.1079-0.0276-0.1495-0.0896-0.03210.02430.04250.04250.04210.13650.06810.1536-12.467-36.496-2.23
21.94090.7187-0.02221.51690.51892.487-0.05590.2837-0.0329-0.1954-0.1860.1351-0.1223-0.370.24190.05520.06620.00710.3174-0.04140.1669-37.403-51.81-14.245
33.5506-0.6131-0.27662.0470.05552.2982-0.2134-0.1097-1.32270.0295-0.03520.40550.5358-0.06310.24860.2403-0.00670.13140.17540.10690.8817-26.012-78.0539.481
43.095-0.1627-0.45332.05730.09261.6434-0.0908-0.9477-0.09820.506-0.044-0.1966-0.02610.33330.13480.21710.0147-0.01610.57570.08640.2239-23.739-53.42828.884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 244
2X-RAY DIFFRACTION2B-1 - 243
3X-RAY DIFFRACTION3C0 - 243
4X-RAY DIFFRACTION4D0 - 243

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