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- PDB-4ad9: Crystal structure of human LACTB2. -

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Basic information

Entry
Database: PDB / ID: 4ad9
TitleCrystal structure of human LACTB2.
ComponentsBETA-LACTAMASE-LIKE PROTEIN 2
KeywordsHYDROLASE / METALLO-BETA LACTAMASE / MITOCHONDRIA
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / single-stranded RNA binding / mitochondrial matrix / zinc ion binding
Similarity search - Function
LACTB2, winged helix domain / : / Beta-lactamase associated winged helix domain / : / 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 ...LACTB2, winged helix domain / : / Beta-lactamase associated winged helix domain / : / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease LACTB2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsAllerston, C.K. / Krojer, T. / Shrestha, B. / Burgess Brown, N. / Chalk, R. / Elkins, J.M. / Filippakopoulos, P. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. ...Allerston, C.K. / Krojer, T. / Shrestha, B. / Burgess Brown, N. / Chalk, R. / Elkins, J.M. / Filippakopoulos, P. / Pike, A.C.W. / Muniz, J.R.C. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Identification of Lactb2, a Metallo-Beta-Lactamase Protein, as a Human Mitochondrial Endoribonuclease
Authors: Allerston, C.K. / Gileadi, O. / Levy, S. / Liveanu, V. / Rohana, M. / Schuster, G.
History
DepositionDec 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Atomic model / Database references / Other
Revision 1.2Mar 16, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE-LIKE PROTEIN 2
B: BETA-LACTAMASE-LIKE PROTEIN 2
C: BETA-LACTAMASE-LIKE PROTEIN 2
D: BETA-LACTAMASE-LIKE PROTEIN 2
E: BETA-LACTAMASE-LIKE PROTEIN 2
F: BETA-LACTAMASE-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,66622
Polymers197,6326
Non-polymers1,03316
Water19,0061055
1
A: BETA-LACTAMASE-LIKE PROTEIN 2
B: BETA-LACTAMASE-LIKE PROTEIN 2
C: BETA-LACTAMASE-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,27110
Polymers98,8163
Non-polymers4557
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-250.6 kcal/mol
Surface area36430 Å2
MethodPISA
2
D: BETA-LACTAMASE-LIKE PROTEIN 2
E: BETA-LACTAMASE-LIKE PROTEIN 2
F: BETA-LACTAMASE-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,39512
Polymers98,8163
Non-polymers5799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-251.3 kcal/mol
Surface area36540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.470, 95.690, 135.760
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BETA-LACTAMASE-LIKE PROTEIN 2 / LACTB2


Mass: 32938.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q53H82, Hydrolases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1055 / 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: 3.38 Å3/Da / Density % sol: 63 %
Description: SUBSTRUCTURE SOLVED FROM THIOMERSAL SOAK, THEN USED FOR RIGID-BODY REFINEMENT USING REFMAC.
Crystal growpH: 7
Details: 0.20M NABR, 0.1 M BTPROP PH 6.5, 20.0% PEG 3350, 10.0% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→46.2 Å / Num. obs: 77582 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 52.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.58→2.72 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.6→46.85 Å / Cor.coef. Fo:Fc: 0.9312 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.404 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.249
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=14221. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=14221. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1957 2.52 %RANDOM
Rwork0.1775 ---
obs0.1787 77581 99.18 %-
Displacement parametersBiso mean: 46.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.5139 Å20 Å23.4054 Å2
2---2.6426 Å20 Å2
3---4.1566 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13126 0 28 1055 14209
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113415HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1418226HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6181SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes324HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1962HARMONIC5
X-RAY DIFFRACTIONt_it13415HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1852SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15523SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2653 147 2.71 %
Rwork0.2096 5277 -
all0.2111 5424 -
obs--99.18 %
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)
11.5176-0.3799-0.30661.02030.47742.6143-0.06980.10650.1099-0.0867-0.05070.029-0.18570.13590.12050.0194-0.0707-0.1064-0.18870.026-0.128717.321874.471934.6853
21.2534-0.16590.65372.5701-1.88852.85910.00390.60280.12490.0216-0.3448-0.38840.02590.88850.3409-0.2976-0.04120.0360.23210.1381-0.289254.09666.577934.262
31.9465-0.0771.17241.0859-0.17621.86150.0256-0.0684-0.06990.0951-0.020.01060.0191-0.0356-0.00570.0889-0.0096-0.0381-0.19440.0075-0.176532.939953.198960.7694
41.95180.54890.40161.02890.23581.59730.08070.0502-0.08020.24470.0045-0.10310.32360.2589-0.08520.11610.1165-0.0831-0.1922-0.0529-0.199813.553921.788326.2859
50.9226-0.38440.15822.6462-0.44223.1513-0.0015-0.0270.0266-0.11040.1171-0.30030.32421.1697-0.1156-0.33350.2007-0.02940.2938-0.1594-0.257838.527529.457-0.459
60.7538-0.0322-0.25561.08690.20333.070200.0310.0304-0.02570.04110.0779-0.0789-0.0365-0.0411-0.02030.0106-0.0796-0.15190.0008-0.09014.914243.0196-2.898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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