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- PDB-2i3o: Crystal structure of gamma-glutamyl transferase related protein f... -

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Basic information

Entry
Database: PDB / ID: 2i3o
TitleCrystal structure of gamma-glutamyl transferase related protein from Thermoplasma acidophilum
ComponentsGamma-glutamyltransferase related protein
KeywordsTRANSFERASE / Gamma-glutamyl transferase related protein / Thermoplasma acidophilum / 6324d / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology: / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal / Gamma-glutamyltransferase related protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsRao, K.N. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of gamma-glutamyl transferase related protein from Thermoplasma acidophilum
Authors: Rao, K.N. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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-glutamyltransferase related protein
B: Gamma-glutamyltransferase related protein
C: Gamma-glutamyltransferase related protein
D: Gamma-glutamyltransferase related protein


Theoretical massNumber of molelcules
Total (without water)230,3164
Polymers230,3164
Non-polymers00
Water15,979887
1
A: Gamma-glutamyltransferase related protein
B: Gamma-glutamyltransferase related protein


Theoretical massNumber of molelcules
Total (without water)115,1582
Polymers115,1582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-12 kcal/mol
Surface area32800 Å2
MethodPISA
2
C: Gamma-glutamyltransferase related protein
D: Gamma-glutamyltransferase related protein


Theoretical massNumber of molelcules
Total (without water)115,1582
Polymers115,1582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.080, 95.471, 119.040
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-glutamyltransferase related protein


Mass: 57578.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Magnesium Formate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 156657 / Num. obs: 156657 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.5
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 15286 / Rsym value: 0.38 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→30.47 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 92146.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed in remark 465 and atoms listed in remark 470 were not modeled due to lack of electron density. Residue ASN254 in all four chains does not have good geometry. However, they ...Details: Residues listed in remark 465 and atoms listed in remark 470 were not modeled due to lack of electron density. Residue ASN254 in all four chains does not have good geometry. However, they fit the electron density very well. Residual densities near the active sites have been modeled as water (39, 40, 45, 167) but they could be metal ions. N terminal Selenomethionine is visible only in chains A and D.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3836 2.5 %RANDOM
Rwork0.183 ---
obs0.183 151643 96.3 %-
all-151643 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6224 Å2 / ksol: 0.369856 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.53 Å2
2--0.7 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.03→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15495 0 0 887 16382
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 574 2.5 %
Rwork0.2 22791 -
obs--89.3 %

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