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- PDB-5c6u: Rv3722c aminotransferase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5c6u
TitleRv3722c aminotransferase from Mycobacterium tuberculosis
ComponentsAminotransferase
KeywordsTRANSFERASE / structural genomics / APC112018 / aspartate aminotransferase / AAT superfamily / pyridoxal phosphate / PLP / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / extracellular region
Similarity search - Function
Aspartate aminotransferase Ic / Aspartate amino-transferase / 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 ...Aspartate aminotransferase Ic / Aspartate amino-transferase / 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
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Aspartate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsOSIPIUK, J. / Hatzos-Skintges, C. / Jedrzejczak, R. / Babnigg, G. / Sacchettini, J. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: to be published
Title: Rv3722c aminotransferase from Mycobacterium tuberculosis.
Authors: OSIPIUK, J. / Hatzos-Skintges, C. / Jedrzejczak, R. / Babnigg, G. / Sacchettini, J. / JOACHIMIAK, A. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) / ...Authors: OSIPIUK, J. / Hatzos-Skintges, C. / Jedrzejczak, R. / Babnigg, G. / Sacchettini, J. / JOACHIMIAK, A. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) / Midwest Center for Structural Genomics (MCSG)
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 2, 2025Group: 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

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4394
Polymers48,0611
Non-polymers3783
Water7,566420
1
A: Aminotransferase
hetero molecules

A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8778
Polymers96,1222
Non-polymers7556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6430 Å2
ΔGint-64 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.341, 64.788, 51.175
Angle α, β, γ (deg.)90.00, 101.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

21A-918-

HOH

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Components

#1: Protein Aminotransferase / Rv3722c protein


Mass: 48060.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3722c, LH57_20280 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69689
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M sodium chloride, 0.1 M sodium phosphate / citric acid buffer, 10% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 40320 / Num. obs: 40320 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.058 / Rrim(I) all: 0.112 / Χ2: 1.471 / Net I/av σ(I): 15.429 / Net I/σ(I): 8.8 / Num. measured all: 146991
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.862.80.5031.9718530.7410.3550.6190.76893.4
1.86-1.93.10.45920320.7740.3060.5540.80299.5
1.9-1.933.30.43319750.8070.2790.5160.949100
1.93-1.973.70.33420480.9040.2020.3910.931100
1.97-2.013.80.27919930.9210.1660.3250.956100
2.01-2.063.80.2420110.9490.1430.281.045100
2.06-2.113.80.21720190.950.130.2531.189100
2.11-2.173.80.18320150.970.1090.2131.224100
2.17-2.233.80.15720400.9770.0940.1831.297100
2.23-2.313.80.1520040.9760.0890.1741.437100
2.31-2.393.80.13320010.9780.0790.1551.46100
2.39-2.483.80.12420190.980.0740.1441.576100
2.48-2.63.80.11220310.9830.0670.131.578100
2.6-2.733.80.10120220.9870.060.1171.62100
2.73-2.93.80.08820340.990.0520.1031.718100
2.9-3.133.80.07620040.9910.0460.0891.738100
3.13-3.443.70.06720520.9940.040.0781.674100
3.44-3.943.70.06420380.9930.0380.0751.729100
3.94-4.973.60.05220420.9960.0320.0611.80399.9
4.97-503.60.05620870.9960.0330.0653.41399.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→35.2 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.492 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17495 2032 5 %RANDOM
Rwork0.14047 ---
obs0.1422 38287 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20.12 Å2
2--0.62 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.83→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 22 420 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193530
X-RAY DIFFRACTIONr_bond_other_d0.0010.023403
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9884829
X-RAY DIFFRACTIONr_angle_other_deg0.79437846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7223.671158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5371527
X-RAY DIFFRACTIONr_chiral_restr0.0890.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
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_it1.0951.521754
X-RAY DIFFRACTIONr_mcbond_other1.0861.5181753
X-RAY DIFFRACTIONr_mcangle_it1.6862.2742201
X-RAY DIFFRACTIONr_mcangle_other1.6872.2762202
X-RAY DIFFRACTIONr_scbond_it1.8351.7691775
X-RAY DIFFRACTIONr_scbond_other1.8371.771772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.982.5612604
X-RAY DIFFRACTIONr_long_range_B_refined5.3213.7834380
X-RAY DIFFRACTIONr_long_range_B_other5.08613.0084168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 139 -
Rwork0.218 2611 -
obs--92.5 %
Refinement TLS params.Method: refined / Origin x: 14.5244 Å / Origin y: 0.56 Å / Origin z: 22.2623 Å
111213212223313233
T0.0027 Å20.0008 Å2-0.0013 Å2-0.0087 Å20.0035 Å2--0.0067 Å2
L0.2085 °2-0.0718 °20.0717 °2-0.1531 °20.0238 °2--0.1318 °2
S0.0061 Å °0.0277 Å °0.0303 Å °0.0106 Å °-0.0052 Å °-0.0258 Å °0.0152 Å °0.0202 Å °-0.0009 Å °

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