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- PDB-6j3i: Structure of LmbA2991T421A -

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Basic information

Entry
Database: PDB / ID: 6j3i
TitleStructure of LmbA2991T421A
ComponentsGamma-glutamyltranspeptidase
KeywordsTRANSFERASE / LmbA2991 / GGT2991 / LmbA-like glutamyltranspeptidase homologues
Function / homology: / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal / Gamma-glutamyltranspeptidase
Function and homology information
Biological speciesStreptomyces lincolnensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21520102004, 31430005, 81302674 and 21472231 China
CitationJournal: To Be Published
Title: Structure of LmbA2991T421A
Authors: Song, Y.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)130,2472
Polymers130,2472
Non-polymers00
Water2,774154
1
A: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)65,1231
Polymers65,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)65,1231
Polymers65,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.352, 113.209, 116.756
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 Gamma-glutamyltranspeptidase


Mass: 65123.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lincolnensis (bacteria) / Gene: SLCG_6815, SLINC_6827 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A1B1MKD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 8.0, 28%(w/v) Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 45004 / % possible obs: 100 % / Redundancy: 10.6 % / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NLZ

2nlz


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.689 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.585 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25507 2261 5 %RANDOM
Rwork0.21386 ---
obs0.21592 42570 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.672 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-0 Å2-0 Å2
2---2.98 Å20 Å2
3---5.72 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8595 0 0 154 8749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198823
X-RAY DIFFRACTIONr_bond_other_d0.0060.028061
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.95512075
X-RAY DIFFRACTIONr_angle_other_deg1.014318566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7751160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80722.62355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48151217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5791575
X-RAY DIFFRACTIONr_chiral_restr0.0780.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021848
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_it0.7462.5074652
X-RAY DIFFRACTIONr_mcbond_other0.7462.5074651
X-RAY DIFFRACTIONr_mcangle_it1.3053.7575808
X-RAY DIFFRACTIONr_mcangle_other1.3053.7575809
X-RAY DIFFRACTIONr_scbond_it0.6572.5444171
X-RAY DIFFRACTIONr_scbond_other0.6572.5444172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.153.7826268
X-RAY DIFFRACTIONr_long_range_B_refined2.50229.359755
X-RAY DIFFRACTIONr_long_range_B_other2.49529.3489749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 155 -
Rwork0.27 3103 -
obs--99.24 %

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