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- PDB-6q1s: A hypothetical aminotransferase from Mycobacterium tuberculosis, ... -

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Basic information

Entry
Database: PDB / ID: 6q1s
TitleA hypothetical aminotransferase from Mycobacterium tuberculosis, alpha-ketoglutarate and PMP bound form
ComponentsProbable amino acid aminotransferase
KeywordsTRANSFERASE / Mycobacterium / aminotransferase / hypothetical protein / PLP-dependent enzyme
Function / homology
Function and homology information


aminodeoxychorismate lyase / 4-amino-4-deoxychorismate lyase activity / 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 ...aminodeoxychorismate lyase / 4-amino-4-deoxychorismate lyase activity / 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
2-OXOGLUTARIC ACID / CITRIC ACID / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Bifunctional aminodeoxychorismate lyase / D-amino acid transaminase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
C: Probable amino acid aminotransferase
D: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,32814
Polymers125,3674
Non-polymers1,96110
Water5,513306
1
A: Probable amino acid aminotransferase
B: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4726
Polymers62,6842
Non-polymers7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-23 kcal/mol
Surface area22250 Å2
MethodPISA
2
C: Probable amino acid aminotransferase
D: Probable amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8568
Polymers62,6842
Non-polymers1,1736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-25 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.545, 202.257, 48.121
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 9 or (resid 10...
21(chain B and (resid 0 through 9 or (resid 10...
31(chain C and (resid 0 through 13 or (resid 14...
41(chain D and (resid 0 through 9 or (resid 10...

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
11ALAALAILEILE(chain A and (resid 0 through 9 or (resid 10...AA0 - 92 - 11
12LEULEUGLNGLN(chain A and (resid 0 through 9 or (resid 10...AA10 - 1112 - 13
13ALAALAARGARG(chain A and (resid 0 through 9 or (resid 10...AA0 - 2892 - 291
14ALAALAARGARG(chain A and (resid 0 through 9 or (resid 10...AA0 - 2892 - 291
15ALAALAARGARG(chain A and (resid 0 through 9 or (resid 10...AA0 - 2892 - 291
16ALAALAARGARG(chain A and (resid 0 through 9 or (resid 10...AA0 - 2892 - 291
21ALAALAILEILE(chain B and (resid 0 through 9 or (resid 10...BB0 - 92 - 11
22LEULEUGLNGLN(chain B and (resid 0 through 9 or (resid 10...BB10 - 1112 - 13
23ASNASNARGARG(chain B and (resid 0 through 9 or (resid 10...BB-1 - 2891 - 291
24ASNASNARGARG(chain B and (resid 0 through 9 or (resid 10...BB-1 - 2891 - 291
25ASNASNARGARG(chain B and (resid 0 through 9 or (resid 10...BB-1 - 2891 - 291
26ASNASNARGARG(chain B and (resid 0 through 9 or (resid 10...BB-1 - 2891 - 291
31ALAALAGLYGLY(chain C and (resid 0 through 13 or (resid 14...CC0 - 132 - 15
32METMETMETMET(chain C and (resid 0 through 13 or (resid 14...CC1416
33ALAALAARGARG(chain C and (resid 0 through 13 or (resid 14...CC0 - 2892 - 291
34ALAALAARGARG(chain C and (resid 0 through 13 or (resid 14...CC0 - 2892 - 291
35ALAALAARGARG(chain C and (resid 0 through 13 or (resid 14...CC0 - 2892 - 291
41ALAALAILEILE(chain D and (resid 0 through 9 or (resid 10...DD0 - 92 - 11
42LEULEUGLNGLN(chain D and (resid 0 through 9 or (resid 10...DD10 - 1112 - 13
43ALAALAARGARG(chain D and (resid 0 through 9 or (resid 10...DD0 - 2892 - 291
44ALAALAARGARG(chain D and (resid 0 through 9 or (resid 10...DD0 - 2892 - 291
45ALAALAARGARG(chain D and (resid 0 through 9 or (resid 10...DD0 - 2892 - 291
46ALAALAARGARG(chain D and (resid 0 through 9 or (resid 10...DD0 - 2892 - 291

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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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
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: 0.97937 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.36
ReflectionResolution: 2→50 Å / Num. obs: 83120 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.106 / Rrim(I) all: 0.211 / Χ2: 0.506 / Net I/σ(I): 2.5 / Num. measured all: 301172
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.41.11232820.2970.7681.3620.4278.4
2.03-2.072.71.07136950.3580.6981.2880.4485.9
2.07-2.112.90.95638390.3870.6151.1450.44390.8
2.11-2.153.20.91341260.4670.5541.0750.43796.5
2.15-2.23.50.85542450.5290.511.0020.46499
2.2-2.253.70.77241760.5940.4510.8990.45699.8
2.25-2.313.80.72243060.9790.4210.840.46199.9
2.31-2.373.80.6442550.7020.3710.7430.46299.9
2.37-2.443.60.58642150.6840.3550.6880.45499.7
2.44-2.523.80.48942660.8270.2790.5650.45499.9
2.52-2.613.70.41442280.8460.2440.4830.45299.9
2.61-2.7140.37942790.8670.2110.4350.4799.9
2.71-2.843.90.30943110.9040.1740.3560.489100
2.84-2.993.90.23242430.9450.1320.2680.489100
2.99-3.173.70.17442850.9630.1040.2040.521100
3.17-3.423.80.12442470.9770.0730.1450.55799.7
3.42-3.7640.09842350.9860.0550.1130.57899.6
3.76-4.313.90.07642820.990.0440.0880.63699.9
4.31-5.433.80.06542910.9910.0380.0750.61599.9
5.43-504.10.06443140.9940.0360.0740.6699.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q1Q

6q1q


Resolution: 2.3→48.121 Å / Cross valid method: THROUGHOUT / σ(F): 167.61 / Phase error: 34.2
RfactorNum. reflection% reflection
Rfree0.2266 2934 5.23 %
Rwork0.2049 --
obs0.215 56131 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.74 Å2 / Biso mean: 25.4113 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 2.3→48.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8578 0 130 306 9014
Biso mean--27.4 27.04 -
Num. residues----1133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028870
X-RAY DIFFRACTIONf_angle_d0.60312100
X-RAY DIFFRACTIONf_chiral_restr0.0421398
X-RAY DIFFRACTIONf_plane_restr0.0051574
X-RAY DIFFRACTIONf_dihedral_angle_d17.8165324
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5206X-RAY DIFFRACTION12.872TORSIONAL
12B5206X-RAY DIFFRACTION12.872TORSIONAL
13C5206X-RAY DIFFRACTION12.872TORSIONAL
14D5206X-RAY DIFFRACTION12.872TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3007-2.34040.27311340.25692654278895
2.3404-2.38290.28151230.262700282396
2.3829-2.42880.31961460.25742629277595
2.4288-2.47830.3061570.24522636279394
2.4783-2.53220.3281280.24132684281295
2.5322-2.59110.2631440.24272606275095
2.5911-2.65590.27471420.23112744288695
2.6559-2.72770.29111320.23942615274795
2.7277-2.80790.24951550.22952668282395
2.8079-2.89850.27011510.22722630278195
2.8985-3.00210.27221780.21892660283894
3.0021-3.12220.25781510.21222623277495
3.1222-3.26430.19911400.20242669280995
3.2643-3.43630.2381650.2072672283794
3.4363-3.65140.21561420.20222619276195
3.6514-3.93310.2071300.18982679280995
3.9331-4.32840.17461590.17142662282194
4.3284-4.95370.17271420.16482639278195
4.9537-6.2370.18611510.1752667281894
6.237-39.01420.42831560.2712699285595
Refinement TLS params.Method: refined / Origin x: 10.4944 Å / Origin y: -0.3465 Å / Origin z: -28.9497 Å
111213212223313233
T0.1286 Å2-0.0297 Å20.0111 Å2-0.3005 Å20.0064 Å2--0.1189 Å2
L0.489 °2-0.1395 °20.1132 °2-0.3113 °2-0.0664 °2--0.3893 °2
S-0.0062 Å °-0.0125 Å °0.0153 Å °-0.019 Å °0.0158 Å °-0.0375 Å °-0.0106 Å °0.0368 Å °-0.0048 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 289
2X-RAY DIFFRACTION1allA290 - 291
3X-RAY DIFFRACTION1allB-1 - 289
4X-RAY DIFFRACTION1allB290 - 291
5X-RAY DIFFRACTION1allC0 - 289
6X-RAY DIFFRACTION1allC290 - 291
7X-RAY DIFFRACTION1allD0 - 289
8X-RAY DIFFRACTION1allD290 - 291
9X-RAY DIFFRACTION1allS1 - 377
10X-RAY DIFFRACTION1allE1 - 3

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