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- PDB-3mdn: Structure of glutamine aminotransferase class-II domain protein (... -

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Basic information

Entry
Database: PDB / ID: 3mdn
TitleStructure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi
ComponentsGlutamine aminotransferase class-II domain protein
KeywordsTRANSFERASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


glutamine metabolic process / transferase activity
Similarity search - Function
Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine amidotransferases class-II domain protein
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine aminotransferase class-II domain protein
B: Glutamine aminotransferase class-II domain protein
C: Glutamine aminotransferase class-II domain protein
D: Glutamine aminotransferase class-II domain protein


Theoretical massNumber of molelcules
Total (without water)122,4014
Polymers122,4014
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-10 kcal/mol
Surface area33870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.367, 72.960, 106.722
Angle α, β, γ (deg.)90.000, 91.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamine aminotransferase class-II domain protein


Mass: 30600.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Gene: SPO2029 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LRU5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 25% PEG 3350, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→40 Å / Num. obs: 59569 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.063 / Χ2: 1.283 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.20.6929661.3151100
2.14-2.186.20.57329371.2891100
2.18-2.226.30.51230031.3161100
2.22-2.266.30.45529341.3081100
2.26-2.316.30.41629701.3581100
2.31-2.376.30.35229721.3621100
2.37-2.426.30.31629661.3981100
2.42-2.496.30.27329761.4011100
2.49-2.566.30.22129621.3761100
2.56-2.656.30.18829691.411100
2.65-2.746.30.14929801.3951100
2.74-2.856.30.12129661.3241100
2.85-2.986.30.10229781.3171100
2.98-3.146.30.07829991.2611100
3.14-3.336.20.06430111.1971100
3.33-3.596.20.05329631.1991100
3.59-3.956.10.0530051.132199.9
3.95-4.525.10.0329810.943199.6
4.52-5.75.70.04430021.003199.4
5.7-405.60.04930291.239197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.796 / SU B: 12.584 / SU ML: 0.148 / SU R Cruickshank DPI: 0.213 / SU Rfree: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3004 5.1 %RANDOM
Rwork0.206 ---
obs0.208 59479 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.43 Å2 / Biso mean: 31.206 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-2.02 Å2
2---1.01 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6811 0 0 36 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217018
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9219530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.56621.433349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94215973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7371572
X-RAY DIFFRACTIONr_chiral_restr0.1040.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215601
X-RAY DIFFRACTIONr_mcbond_it0.9081.54314
X-RAY DIFFRACTIONr_mcangle_it1.65926810
X-RAY DIFFRACTIONr_scbond_it2.37332704
X-RAY DIFFRACTIONr_scangle_it3.6544.52720
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 190 -
Rwork0.261 3785 -
all-3975 -
obs--90.4 %
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)
11.77661.25550.38232.6813-0.75532.4097-0.15520.0034-0.0556-0.09830.1839-0.1033-0.0359-0.0539-0.02860.14140.0448-0.07870.19680.02810.095130.6945.96971.664
22.45961.45741.97023.3504-0.13474.2627-0.05920.28280.1594-0.2835-0.00420.04040.00250.7660.06350.07710.0214-0.03620.3839-0.02180.059959.527-27.28765.349
31.8425-1.55170.96573.5898-0.48162.2175-0.1482-0.12910.07610.31620.22570.0482-0.1335-0.2497-0.07750.12190.0152-0.03590.25280.05920.077834.867-27.74594.203
42.0192-1.42550.44172.68770.40312.334-0.14110.0841-0.10240.19110.16320.1376-0.07380.0606-0.02210.2245-0.0764-0.14260.2308-0.00880.146664.1814.97490.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 257
2X-RAY DIFFRACTION1A273 - 283
3X-RAY DIFFRACTION2B2 - 257
4X-RAY DIFFRACTION2B273 - 278
5X-RAY DIFFRACTION3C2 - 257
6X-RAY DIFFRACTION3C273 - 283
7X-RAY DIFFRACTION4D2 - 259
8X-RAY DIFFRACTION4D273 - 280

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