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- PDB-4riz: The crystal structure of Y333Q mutant pyridoxal-dependent decarbo... -

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Basic information

Entry
Database: PDB / ID: 4riz
TitleThe crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745
ComponentsPyridoxal-dependent decarboxylase
KeywordsLYASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / A/B/A FOLD / CYTOSOLIC
Function / homology
Function and homology information


sulfinoalanine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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, domain 1 - #170 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Pyridoxal-dependent decarboxylase
Similarity search - Component
Biological speciesSphaerobacter thermophilus DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of y333q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Authors: Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal-dependent decarboxylase
B: Pyridoxal-dependent decarboxylase
C: Pyridoxal-dependent decarboxylase
D: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,50414
Polymers212,3224
Non-polymers1,18210
Water14,268792
1
A: Pyridoxal-dependent decarboxylase
B: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7318
Polymers106,1612
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-133 kcal/mol
Surface area30590 Å2
MethodPISA
2
C: Pyridoxal-dependent decarboxylase
D: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7726
Polymers106,1612
Non-polymers6114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-128 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.411, 124.659, 131.849
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyridoxal-dependent decarboxylase


Mass: 53080.449 Da / Num. of mol.: 4 / Mutation: Y333Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria)
Strain: DSM 20745 / S 6022 / Gene: Sthe_2364 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D1C7D8, glutamate decarboxylase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG1000, 0.1M TRis:HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2012 / Details: MIRRORS
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 112112 / Num. obs: 112112 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.095 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 5609 / Rsym value: 0.095 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RIT

4rit


Resolution: 2.2→39.582 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 5610 5.01 %
Rwork0.1574 --
obs0.1595 111927 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14498 0 75 792 15365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714922
X-RAY DIFFRACTIONf_angle_d0.84520318
X-RAY DIFFRACTIONf_dihedral_angle_d13.65459
X-RAY DIFFRACTIONf_chiral_restr0.0362284
X-RAY DIFFRACTIONf_plane_restr0.0052676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.2210.27091780.23473218339891
2.221-2.24710.30891790.22663538371799
2.2471-2.27450.25881860.215535543740100
2.2745-2.30330.2622010.201635493750100
2.3033-2.33360.25552000.202235253725100
2.3336-2.36550.25771680.199735173685100
2.3655-2.39930.2332020.184635903792100
2.3993-2.43510.26712010.180534833684100
2.4351-2.47320.2591920.183335623754100
2.4732-2.51370.2061710.178435663737100
2.5137-2.55710.26611820.17235773759100
2.5571-2.60360.21331800.169735193699100
2.6036-2.65360.22471820.169335833765100
2.6536-2.70780.23991830.169235463729100
2.7078-2.76660.21791860.164435513737100
2.7666-2.8310.242000.172135613761100
2.831-2.90180.22911800.164135723752100
2.9018-2.98020.20851860.160935513737100
2.9802-3.06780.18971790.161635763755100
3.0678-3.16680.22531860.16435793765100
3.1668-3.280.20041920.167135533745100
3.28-3.41120.19252110.155835043715100
3.4112-3.56640.2042000.151635823782100
3.5664-3.75430.17551970.139635433740100
3.7543-3.98930.14891940.134535473741100
3.9893-4.29690.15921820.12593591377399
4.2969-4.72870.16011720.12173559373199
4.7287-5.41150.14461700.13423578374899
5.4115-6.81230.18171770.15593569374699
6.8123-39.58870.15091930.13523574376797
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)
12.1154-0.95890.08211.56630.081.49760.18910.347-0.3488-0.6223-0.20320.14050.24380.05550.00620.40390.0107-0.00950.2778-0.02680.2477-8.63723.977228.9558
20.8218-0.63010.01971.95410.48130.46990.02510.1233-0.1963-0.3235-0.09890.55750.1507-0.14010.05670.2498-0.0476-0.09570.2739-0.020.3262-25.343210.471438.9071
3-0.0554-0.1841-0.39180.60410.031.1593-0.00770.02720.0538-0.0110.0233-0.2038-0.04090.1398-0.00210.1348-0.02220.00660.22030.00140.2467-3.502821.710854.0865
42.3176-1.59910.6371.9664-0.51990.9765-0.1322-0.2216-0.10690.47880.14140.03380.04070.06830.0280.3471-0.0116-0.04360.2668-0.00640.2758-13.381720.011776.2154
50.8832-0.33890.1031.3722-0.12480.3738-0.0717-0.1050.06550.2540.05770.0658-0.012-0.03980.00180.1610.00010.0320.1991-0.00990.1744-18.958130.081670.5495
60.99810.01670.6031.12441.13561.6572-0.07660.04140.1309-0.0382-0.01240.0278-0.18430.06160.06770.1819-0.0293-0.01590.19370.02220.2396-15.00432.28254.3941
70.41620.1372-0.50070.71260.08581.0224-0.0718-0.0117-0.10020.08680.0529-0.4203-0.01660.2690.00180.1395-0.0122-0.03550.26720.01710.30681.965419.735560.2421
81.7077-0.3077-0.21731.01690.21151.23080.0143-0.11780.1701-0.0390.01460.2544-0.086-0.2529-0.04350.1332-0.0059-0.02840.2210.01750.2366-32.780431.359950.3883
90.81270.113-0.6721.0184-0.1691.3210.0439-0.0840.0322-0.1161-0.020.32740.0007-0.3274-0.04550.1683-0.0185-0.04130.27310.0080.3053-37.832227.812347.656
100.72450.70630.52531.3418-0.1391.16350.02320.13270.2509-0.5953-0.14170.0838-0.18580.01380.12650.28670.00050.00160.26480.00810.223-14.258524.87529.9522
110.6545-0.74080.18742.2158-0.80060.26050.04660.09460.1718-0.1433-0.0966-0.3851-0.08870.16260.02780.2008-0.02530.05970.29920.04020.30563.554716.60639.0337
120.5697-0.45920.47350.8435-0.0420.4499-0.0054-0.0732-0.09880.00040.06580.25580.0509-0.1194-0.0710.1375-0.0287-0.01260.22510.02410.251-19.87754.31648.9092
131.8346-0.116-0.56862.01980.55342.4571-0.0563-0.1417-0.02540.33070.04540.12750.048-0.00240.00020.19940.00480.00920.21730.01970.1902-13.63566.42373.8315
141.1058-0.0614-0.12131.64080.46660.4909-0.0455-0.0929-0.03730.29340.0102-0.26790.010.12950.03690.2049-0.0001-0.05420.22370.04660.245-2.1523-4.21369.5326
150.98350.1275-0.58520.9997-1.20311.5006-0.0227-0.0006-0.0863-0.1020.0241-0.07780.20270.0254-0.00790.2065-0.0006-0.02430.1839-0.00260.2766-6.6397-6.375353.2449
160.19020.01140.32870.4996-0.30670.9039-0.0683-0.05680.05290.04740.16680.3417-0.0214-0.397-0.09070.13640.0050.02880.2940.04130.318-23.82725.888560.2565
171.5689-0.16420.03441.1034-0.56681.36650.0922-0.0272-0.272-0.1669-0.2253-0.40490.10860.40290.08220.1660.01730.06370.30610.0560.382412.6603-3.819848.0974
180.72870.08230.06861.7206-0.14430.64370.0505-0.0501-0.0240.133-0.0515-0.04890.02180.0617-0.00930.3260.0159-0.0210.187-0.01140.1464-22.165-55.745413.4422
190.77810.17820.0722.0809-0.23640.70110.01590.07020.0823-0.13140.01960.1917-0.0773-0.0408-0.0440.38460.0253-0.03050.18590.0040.2004-32.4714-40.87590.0092
201.2971-0.1316-0.47370.7423-0.31951.54720.13070.09580.135-0.0676-0.1034-0.1976-0.09820.2566-0.03950.29980.01120.00340.22320.00370.217-5.8669-39.0953-1.5285
211.21950.654-0.41371.5271-0.65810.68590.1391-0.3630.03980.5388-0.1659-0.2964-0.04710.3352-0.01740.6316-0.0501-0.20260.38440.00280.3415-10.1874-48.435827.1451
220.32960.7378-0.07972.34940.050.06150.0938-0.06560.18840.7688-0.0180.3095-0.1040.0601-0.08690.6449-0.01060.02460.3041-0.01790.2372-30.1847-52.950729.5801
230.71130.15160.52181.0472-0.18240.53720.01990.126-0.016-0.1891-0.025-0.05610.1130.11680.00620.37470.0389-0.01530.22080.01250.202-21.9502-64.83553.8815
240.98170.2583-0.28791.6819-0.02530.7593-0.03610.121-0.0445-0.22510.07350.38550.1467-0.1241-0.0390.4152-0.0056-0.08930.209-0.01360.2791-43.1235-72.6020.637
250.7642-0.13290.74921.6944-0.31080.91240.02440.1338-0.0126-0.2336-0.0302-0.1620.0280.10840.04620.44160.029-0.00330.23120.00440.2261-25.2052-66.00540.6471
261.37110.3457-0.01851.271-0.18651.11660.0864-0.2722-0.1120.3309-0.05660.3010.0241-0.221-0.00370.48320.01390.04650.30190.0060.2874-42.5934-73.694327.1977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 167 )
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 191 )
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 281 )
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 312 )
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 355 )
8X-RAY DIFFRACTION8chain 'A' and (resid 356 through 433 )
9X-RAY DIFFRACTION9chain 'A' and (resid 434 through 477 )
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 38 )
11X-RAY DIFFRACTION11chain 'B' and (resid 39 through 96 )
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 180 )
14X-RAY DIFFRACTION14chain 'B' and (resid 181 through 281 )
15X-RAY DIFFRACTION15chain 'B' and (resid 282 through 312 )
16X-RAY DIFFRACTION16chain 'B' and (resid 313 through 354 )
17X-RAY DIFFRACTION17chain 'B' and (resid 355 through 477 )
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 191 )
19X-RAY DIFFRACTION19chain 'C' and (resid 192 through 354 )
20X-RAY DIFFRACTION20chain 'C' and (resid 355 through 477 )
21X-RAY DIFFRACTION21chain 'D' and (resid 5 through 38 )
22X-RAY DIFFRACTION22chain 'D' and (resid 39 through 96 )
23X-RAY DIFFRACTION23chain 'D' and (resid 97 through 167 )
24X-RAY DIFFRACTION24chain 'D' and (resid 168 through 289 )
25X-RAY DIFFRACTION25chain 'D' and (resid 290 through 354 )
26X-RAY DIFFRACTION26chain 'D' and (resid 355 through 476 )

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