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- PDB-6q1r: A hypothetical aminotransferase from Mycobacterium tuberculosis, ... -

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Basic information

Entry
Database: PDB / ID: 6q1r
TitleA hypothetical aminotransferase from Mycobacterium tuberculosis, PLP-bound form
ComponentsProbable amino acid aminotransferase
KeywordsTRANSFERASE / Mycobacterium / aminotransferase / hypothetical protein / PLP-dependent enzyme
Function / homology
Function and homology information


4-amino-4-deoxychorismate lyase activity / aminodeoxychorismate lyase / D-amino-acid transaminase / carboxylic acid metabolic process / folic acid biosynthetic process / transaminase activity / peptidoglycan biosynthetic process / tetrahydrofolate biosynthetic process / pyridoxal phosphate binding / regulation of cell shape ...4-amino-4-deoxychorismate lyase activity / aminodeoxychorismate lyase / D-amino-acid transaminase / carboxylic acid metabolic process / folic acid biosynthetic process / transaminase activity / peptidoglycan biosynthetic process / tetrahydrofolate biosynthetic process / pyridoxal phosphate binding / regulation of cell shape / plasma membrane / cytosol
Similarity search - Function
Aminodeoxychorismate lyase, class IV / : / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
CITRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Bifunctional aminodeoxychorismate lyase / D-amino acid transaminase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsDuan, L. / Sacchettini, J.
CitationJournal: To Be Published
Title: A hypothetical aminotransferase from Mycobacterium tuberculosis
Authors: Duan, L. / Sacchettini, J.
History
DepositionAug 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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: Probable amino acid aminotransferase
B: Probable amino acid aminotransferase
C: Probable amino acid aminotransferase
D: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,83211
Polymers125,3674
Non-polymers1,4657
Water1,45981
1
A: Probable amino acid aminotransferase
B: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4626
Polymers62,6842
Non-polymers7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-28 kcal/mol
Surface area22560 Å2
MethodPISA
2
C: Probable amino acid aminotransferase
D: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3705
Polymers62,6842
Non-polymers6863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-28 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.431, 203.248, 48.112
Angle α, β, γ (deg.)90.000, 89.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 39 or (resid 40...
21(chain B and (resid 0 through 66 or (resid 67...
31(chain C and (resid 0 through 39 or (resid 40...
41(chain D and (resid 0 through 39 or (resid 40...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 0 through 39 or (resid 40...A0 - 39
121(chain A and (resid 0 through 39 or (resid 40...A40 - 41
131(chain A and (resid 0 through 39 or (resid 40...A0 - 289
141(chain A and (resid 0 through 39 or (resid 40...A0 - 289
151(chain A and (resid 0 through 39 or (resid 40...A0 - 289
161(chain A and (resid 0 through 39 or (resid 40...A0 - 289
211(chain B and (resid 0 through 66 or (resid 67...B0 - 66
221(chain B and (resid 0 through 66 or (resid 67...B67
231(chain B and (resid 0 through 66 or (resid 67...B-1 - 289
241(chain B and (resid 0 through 66 or (resid 67...B-1 - 289
251(chain B and (resid 0 through 66 or (resid 67...B-1 - 289
261(chain B and (resid 0 through 66 or (resid 67...B-1 - 289
311(chain C and (resid 0 through 39 or (resid 40...C0 - 39
321(chain C and (resid 0 through 39 or (resid 40...C40 - 41
331(chain C and (resid 0 through 39 or (resid 40...C0 - 289
341(chain C and (resid 0 through 39 or (resid 40...C0 - 289
351(chain C and (resid 0 through 39 or (resid 40...C0 - 289
361(chain C and (resid 0 through 39 or (resid 40...C0 - 289
411(chain D and (resid 0 through 39 or (resid 40...D0 - 39
421(chain D and (resid 0 through 39 or (resid 40...D40 - 41
431(chain D and (resid 0 through 39 or (resid 40...D-1 - 290
441(chain D and (resid 0 through 39 or (resid 40...D-1 - 290
451(chain D and (resid 0 through 39 or (resid 40...D-1 - 290
461(chain D and (resid 0 through 39 or (resid 40...D-1 - 290

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Components

#1: Protein
Probable amino acid aminotransferase


Mass: 31341.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0812 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79FW0
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34287 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.19 Å2 / Rmerge(I) obs: 0.528 / Rpim(I) all: 0.279 / Rrim(I) all: 0.6 / Χ2: 1.004 / Net I/σ(I): 2 / Num. measured all: 145983
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.32.97916680.1211.8343.5160.50697.3
2.75-2.83.52.59717210.2071.5413.0350.49798.3
2.8-2.853.72.37916950.0231.3862.7670.52198.7
2.85-2.913.92.33916990.2281.3292.7030.54398.7
2.91-2.973.92.04716800.3231.1452.3560.56498.5
2.97-3.043.71.87417070.321.082.1730.58597.9
3.04-3.123.91.63516840.3640.9131.8820.55198.4
3.12-3.24.61.43817590.580.7231.6150.63499.9
3.2-3.34.51.15816980.6090.5911.3050.689100
3.3-3.44.60.97117280.720.4911.0930.72699.9
3.4-3.524.60.88517230.7540.4460.9950.78399.7
3.52-3.664.60.68617320.7940.3460.7710.89999.7
3.66-3.834.50.56616940.8440.2880.6380.97499.5
3.83-4.034.60.48317490.860.2420.5421.15699.7
4.03-4.294.40.38117090.8870.20.4331.1699.3
4.29-4.624.10.28916830.9210.1570.3311.44798.1
4.62-5.084.80.25817510.9440.1280.2891.30499.9
5.08-5.814.80.26917220.950.1320.3010.99999.7
5.81-7.324.60.22617360.9520.1140.2541.04999.5
7.32-504.50.17417490.9620.0890.1963.72598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q1Q

6q1q


Resolution: 2.702→43.485 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.68
RfactorNum. reflection% reflection
Rfree0.2558 1743 5.19 %
Rwork0.2169 --
obs0.219 33555 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.04 Å2 / Biso mean: 50.4739 Å2 / Biso min: 15.19 Å2
Refinement stepCycle: final / Resolution: 2.702→43.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8592 0 92 81 8765
Biso mean--53.15 31.05 -
Num. residues----1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048853
X-RAY DIFFRACTIONf_angle_d0.75412085
X-RAY DIFFRACTIONf_chiral_restr0.0461401
X-RAY DIFFRACTIONf_plane_restr0.0051570
X-RAY DIFFRACTIONf_dihedral_angle_d15.9165315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5236X-RAY DIFFRACTION12.765TORSIONAL
12B5236X-RAY DIFFRACTION12.765TORSIONAL
13C5236X-RAY DIFFRACTION12.765TORSIONAL
14D5236X-RAY DIFFRACTION12.765TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7021-2.78160.36071000.3082154225477
2.7816-2.87130.33751560.30912449260590
2.8713-2.97390.35841440.30032632277696
2.9739-3.0930.31731440.29082626277096
3.093-3.23370.31471450.268127582903100
3.2337-3.40410.30421470.240127562903100
3.4041-3.61730.2681500.229227332883100
3.6173-3.89640.2841610.210927522913100
3.8964-4.28820.21521250.18392743286899
4.2882-4.9080.19651400.16512723286399
4.908-6.18080.22561490.19627522901100
6.1808-43.49050.20261820.17492734291699
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)
10.8868-0.17260.48192.22211.44013.5438-0.03890.0591-0.0455-0.07250.0693-0.0346-0.09960.0351-0.0540.1646-0.02590.04050.32810.06690.196322.3851-5.84773.124
24.3071-0.05811.43983.1942-0.36623.10580.0946-0.2236-0.35490.14330.0593-0.17710.53250.0629-0.14810.38750.06820.04780.33840.06360.307431.4612-35.60518.4741
31.18530.0930.09912.35950.71264.19320.01270.04070.07680.0370.0365-0.0162-0.01250.0236-0.02450.13620.0087-0.01250.35710.02670.1903-10.84084.9081-13.1098
43.90640.318-0.3253.4986-0.32172.3388-0.08060.43140.6248-0.53490.1832-0.1373-0.68960.0966-0.10490.6019-0.0509-0.01860.35730.05770.3941-1.421534.7223-17.9861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 289)A0 - 289
2X-RAY DIFFRACTION2(chain 'B' and resid -1 through 289)B-1 - 289
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 289)C0 - 289
4X-RAY DIFFRACTION4(chain 'D' and resid -1 through 289)D-1 - 289

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