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

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Basic information

Entry
Database: PDB / ID: 6kns
TitleCrystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group I4122)
ComponentsPutative metal-dependent hydrolase
KeywordsHYDROLASE / enzyme / metallo-beta-lactamase fold protein
Function / homology
Function and homology information


Beta-lactamase superfamily domain / 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
Putative metal-dependent hydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)109,00916
Polymers108,3254
Non-polymers68412
Water7,242402
1
A: Putative metal-dependent hydrolase
hetero molecules

A: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,58510
Polymers54,1632
Non-polymers4228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area2990 Å2
ΔGint-199 kcal/mol
Surface area18170 Å2
MethodPISA
2
B: Putative metal-dependent hydrolase
hetero molecules

B: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5058
Polymers54,1632
Non-polymers3426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area2600 Å2
ΔGint-196 kcal/mol
Surface area17900 Å2
MethodPISA
3
C: Putative metal-dependent hydrolase
hetero molecules

C: 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
crystal symmetry operation10_545-x,-y-1,z1
Buried area2440 Å2
ΔGint-172 kcal/mol
Surface area17820 Å2
MethodPISA
4
D: Putative metal-dependent hydrolase
hetero molecules

D: Putative metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5058
Polymers54,1632
Non-polymers3426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area2600 Å2
ΔGint-197 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.378, 106.378, 404.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21B-425-

HOH

31B-454-

HOH

41C-405-

HOH

51C-463-

HOH

61D-429-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLNGLNAA1 - 767 - 82
21METMETGLNGLNBB1 - 767 - 82
31METMETGLNGLNCC1 - 767 - 82
41METMETGLNGLNDD1 - 767 - 82
12THRTHRTRPTRPAA87 - 24293 - 248
22THRTHRTRPTRPBB87 - 24293 - 248
32THRTHRTRPTRPCC87 - 24293 - 248
42THRTHRTRPTRPDD87 - 24293 - 248

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 8000, calcium acetate, sodium acetate

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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: 2.15→30 Å / Num. obs: 61164 / % possible obs: 95.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 33
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.439 / Num. unique obs: 5769 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.817 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 3094 5.1 %RANDOM
Rwork0.168 ---
obs0.1698 57824 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 73.53 Å2 / Biso mean: 28.871 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 0 12 402 7817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217605
X-RAY DIFFRACTIONr_bond_other_d0.0020.024896
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.94110339
X-RAY DIFFRACTIONr_angle_other_deg0.902312002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77924.704338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.152151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5421512
X-RAY DIFFRACTIONr_chiral_restr0.0890.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021547
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1360MEDIUM POSITIONAL0.120.5
2B1360MEDIUM POSITIONAL0.120.5
3C1360MEDIUM POSITIONAL0.160.5
4D1360MEDIUM POSITIONAL0.150.5
1A1570LOOSE POSITIONAL0.325
2B1570LOOSE POSITIONAL0.325
3C1570LOOSE POSITIONAL0.525
4D1570LOOSE POSITIONAL0.415
1A1360MEDIUM THERMAL0.572
2B1360MEDIUM THERMAL0.472
3C1360MEDIUM THERMAL0.582
4D1360MEDIUM THERMAL0.542
1A1570LOOSE THERMAL0.7310
2B1570LOOSE THERMAL0.6310
3C1570LOOSE THERMAL0.7610
4D1570LOOSE THERMAL0.7410
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 207 -
Rwork0.197 4029 -
all-4236 -
obs--91.57 %
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)
10.69160.2061-0.35671.2548-0.26051.4139-0.0095-0.0116-0.01740.0579-0.0401-0.21050.06220.24110.04960.02110.0025-0.01920.1450.00720.050315.788-52.4538.384
21.05970.11530.28831.1-0.06111.58190.0029-0.0601-0.0257-0.01490.0157-0.18070.02870.2321-0.01860.1071-0.00540.00520.1008-0.00920.050516.163-51.194.615
31.05330.0548-0.32380.821-0.13541.3345-0.0213-0.0144-0.0940.04220.00750.05030.134-0.03650.01380.05160.01920.0050.05720.00560.0132-9.184-66.57274.423
41.85960.6895-0.02361.6681-0.07071.2621-0.25890.24630.2611-0.4430.26430.3776-0.0044-0.2465-0.00540.3516-0.0963-0.14580.11940.08890.1304-13.008-43.789-30.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 244
2X-RAY DIFFRACTION2B-1 - 244
3X-RAY DIFFRACTION3C-2 - 244
4X-RAY DIFFRACTION4D-1 - 243

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