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- PDB-6q1q: A hypothetical aminotransferase from Mycobacterium tuberculosis, ... -

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Basic information

Entry
Database: PDB / ID: 6q1q
TitleA hypothetical aminotransferase from Mycobacterium tuberculosis, apo 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 / Bifunctional aminodeoxychorismate lyase / D-amino acid transaminase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3168
Polymers62,6842
Non-polymers6336
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-11 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.383, 66.486, 97.510
Angle α, β, γ (deg.)90.000, 90.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 0 through 194 or resid 201 through 289))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGchain AAA0 - 2892 - 291
21ALAALAGLYGLY(chain B and (resid 0 through 194 or resid 201 through 289))BB0 - 1942 - 196
22PROPROARGARG(chain B and (resid 0 through 194 or resid 201 through 289))BB201 - 289203 - 291

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Components

#1: Protein Probable amino acid aminotransferase


Mass: 31341.764 Da / Num. of mol.: 2
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24452 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.24 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.08 / Rrim(I) all: 0.157 / Χ2: 1.758 / Net I/σ(I): 5.4 / Num. measured all: 89973
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.40.45512020.8120.280.5360.851100
2.44-2.493.50.4512060.7970.2760.530.96499.9
2.49-2.533.60.3912110.8690.2330.4560.98999.8
2.53-2.593.50.35512270.850.2160.4171.09899.8
2.59-2.643.60.34812080.890.2070.4061.16199.9
2.64-2.73.90.31812130.9050.1830.3681.16499.9
2.7-2.773.90.27112200.9290.1560.3131.124100
2.77-2.853.80.25412260.9290.1470.2941.254100
2.85-2.933.80.23712050.9360.1380.2751.33499.9
2.93-3.023.80.20212530.9550.1170.2341.502100
3.02-3.133.80.18811920.9570.110.2191.685100
3.13-3.263.70.15812260.9640.0940.1841.74199.8
3.26-3.413.60.14512130.970.0870.172.13399.6
3.41-3.583.40.13312130.9720.0830.1572.28299.8
3.58-3.813.60.12812240.9750.0770.152.59199.4
3.81-4.13.70.11512360.980.0680.1342.74499.6
4.1-4.523.80.10412140.9820.0610.1212.899.8
4.52-5.173.80.10212420.980.0590.1182.79799.5
5.17-6.513.50.112320.9790.060.1172.299.9
6.51-503.70.08112890.990.0480.0952.60499.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K3W

5k3w


Resolution: 2.4→48.755 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2285 1215 4.97 %
Rwork0.1946 --
obs0.1964 24430 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 48.6238 Å2 / Biso min: 16.37 Å2
Refinement stepCycle: final / Resolution: 2.4→48.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 42 157 4525
Biso mean--61.87 43.16 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034446
X-RAY DIFFRACTIONf_angle_d0.6496055
X-RAY DIFFRACTIONf_chiral_restr0.045702
X-RAY DIFFRACTIONf_plane_restr0.005791
X-RAY DIFFRACTIONf_dihedral_angle_d15.662678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2600X-RAY DIFFRACTION8.33TORSIONAL
12B2600X-RAY DIFFRACTION8.33TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3949-2.49070.27811360.23572501263797
2.4907-2.60410.25531190.229425542673100
2.6041-2.74140.2871090.231326072716100
2.7414-2.91310.29961390.226825712710100
2.9131-3.1380.22941350.226225792714100
3.138-3.45370.26191300.209526172747100
3.4537-3.95330.24031490.184825422691100
3.9533-4.97990.18341620.157825712733100
4.9799-48.7650.19911360.174826732809100
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)
11.2988-0.1677-0.04870.7474-0.01880.40060.0002-0.0178-0.00790.0289-0.01050.0368-0.0110.04450.00250.1713-0.00760.00470.16850.00280.231916.0473-1.59415.3024
20.59690.124-0.32081.6898-0.82221.6536-0.0141-0.18050.0190.4901-0.0510.0496-0.2681-0.08620.03610.42050.00150.01360.3849-0.03430.232210.9647.449535.2466
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 0 through 289)B0 - 289

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