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- PDB-6j3a: Structure of LmbA2991HD -

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Basic information

Entry
Database: PDB / ID: 6j3a
TitleStructure of LmbA2991HD
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: 2.38 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 LmbA2991HD
Authors: Song, Y.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)130,3072
Polymers130,3072
Non-polymers00
Water3,729207
1
A: Gamma-glutamyltranspeptidase

B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)130,3072
Polymers130,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_574-x+1/2,-y+2,z-1/21
Buried area3760 Å2
ΔGint-19 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.440, 113.177, 116.527
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: 65153.270 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.: 207 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH8.0, 28% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.38→81.19 Å / Num. obs: 51650 / % possible obs: 99.4 % / Redundancy: 5.4 % / Net I/σ(I): 8.33
Reflection shellResolution: 2.38→2.42 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.125 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 2588 5 %RANDOM
Rwork0.22367 ---
obs0.22576 49004 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å2-0 Å2-0 Å2
2---3.43 Å20 Å2
3---6.01 Å2
Refinement stepCycle: 1 / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8621 0 0 207 8828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198855
X-RAY DIFFRACTIONr_bond_other_d0.0060.028104
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.95712115
X-RAY DIFFRACTIONr_angle_other_deg0.983318685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64651156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11222.652362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.962151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4021576
X-RAY DIFFRACTIONr_chiral_restr0.0750.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
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_it1.1173.3884636
X-RAY DIFFRACTIONr_mcbond_other1.1183.3884635
X-RAY DIFFRACTIONr_mcangle_it1.8555.0795788
X-RAY DIFFRACTIONr_mcangle_other1.8555.0795789
X-RAY DIFFRACTIONr_scbond_it1.1543.494219
X-RAY DIFFRACTIONr_scbond_other1.1543.494220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9355.186328
X-RAY DIFFRACTIONr_long_range_B_refined3.39639.9929926
X-RAY DIFFRACTIONr_long_range_B_other3.38139.9899911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.378→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 186 -
Rwork0.348 3387 -
obs--94.25 %

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