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- PDB-3cai: Crystal structure of Mycobacterium tuberculosis Rv3778c protein -

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Basic information

Entry
Database: PDB / ID: 3cai
TitleCrystal structure of Mycobacterium tuberculosis Rv3778c protein
ComponentsPOSSIBLE AMINOTRANSFERASE
KeywordsTRANSFERASE / Rv3778c / Aminotransferase
Function / homology
Function and homology information


cell wall / catalytic activity / peptidoglycan-based cell wall / plasma membrane
Similarity search - Function
Cysteine desulfurase-related / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cysteine desulfurase-related / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein Rv3778c / Uncharacterized protein Rv3778c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCovarrubias, A.S. / Larsson, A.M. / Jones, T.A. / Bergfors, T. / Mowbray, S.L. / Unge, T.
CitationJournal: To be published
Title: Structure and biochemical function studies of Mycobacterium tuberculosis essential protein Rv3778c
Authors: Covarrubias, A.S. / Larsson, A.M. / Jones, T.A. / Bergfors, T. / Mowbray, S.L. / Unge, T.
History
DepositionFeb 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE AMINOTRANSFERASE
B: POSSIBLE AMINOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)85,7052
Polymers85,7052
Non-polymers00
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-25.2 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.842, 81.842, 115.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein POSSIBLE AMINOTRANSFERASE / Aminotransferase / putative / Rv3778c


Mass: 42852.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rv3778c / Plasmid: pPCRT7/CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AI
References: UniProt: P72044, UniProt: P9WQ67*PLUS, Transferases; Transferring nitrogenous groups; Transaminases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.27 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 14.4% PEG 5000, 100mM sodium acetate, 10mM NaCl, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→30.95 Å / Num. obs: 70551 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 3.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.94.80.481.549737102950.48100
1.9-2.014.90.3252.34746696710.325100
2.01-2.1550.2334580091820.23100
2.15-2.3250.1743.94293885040.174100
2.32-2.555.10.1384.84015578370.138100
2.55-2.855.20.125.33651770890.12100
2.85-3.295.20.1175.13234462800.117100
3.29-4.025.10.1015.62716252810.101100
4.02-5.695.10.1154.82106641340.115100
5.69-30.954.90.0975.11117622780.09799.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.397 / Cor.coef. Fo:Fc: 0.589
Highest resolutionLowest resolution
Rotation3 Å30.95 Å
Translation3 Å30.95 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C0N

1c0n


Resolution: 1.8→30.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.954 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3556 5 %RANDOM
Rwork0.177 ---
obs0.179 70504 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.258 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 0 617 6581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216083
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9568319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9825813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22522.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61715924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.011562
X-RAY DIFFRACTIONr_chiral_restr0.0780.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024636
X-RAY DIFFRACTIONr_nbd_refined0.1980.23056
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2583
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.227
X-RAY DIFFRACTIONr_mcbond_it0.6921.54070
X-RAY DIFFRACTIONr_mcangle_it1.17826409
X-RAY DIFFRACTIONr_scbond_it1.97132244
X-RAY DIFFRACTIONr_scangle_it3.2754.51910
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 256 -
Rwork0.221 4932 -
all-5188 -
obs--99.94 %

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