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- PDB-6zuj: Human serine racemase holoenzyme from 20% DMSO soak (XChem crysta... -

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Basic information

Entry
Database: PDB / ID: 6zuj
TitleHuman serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).
ComponentsSerine racemase
KeywordsISOMERASE / PLP-dependent / D-serine / forebrain
Function / homology
Function and homology information


serine racemase / threonine racemase activity / D-serine biosynthetic process / serine family amino acid metabolic process / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine metabolic process ...serine racemase / threonine racemase activity / D-serine biosynthetic process / serine family amino acid metabolic process / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine metabolic process / Serine biosynthesis / pyruvate biosynthetic process / L-serine metabolic process / glycine binding / PDZ domain binding / response to organic cyclic compound / pyridoxal phosphate binding / apical part of cell / response to lipopolysaccharide / response to xenobiotic stimulus / neuronal cell body / calcium ion binding / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKoulouris, C.R. / Bax, B.D. / Roe, S.M. / Atack, J.R.
Citation
Journal: Commun Biol / Year: 2022
Title: Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Authors: Koulouris, C.R. / Gardiner, S.E. / Harris, T.K. / Elvers, K.T. / Mark Roe, S. / Gillespie, J.A. / Ward, S.E. / Grubisha, O. / Nicholls, R.A. / Atack, J.R. / Bax, B.D.
#1: Journal: Biorxiv / Year: 2021
Title: Tyrosine 121 moves revealing a druggable pocket that couples catalysis to ATP-binding in serine racemase
Authors: Koulouris, C.R. / Gardiner, S.E. / Harris, T.K. / Elvers, K.T. / Roe, S.M. / Gillespie, J.A. / Ward, S.E. / Grubisha, O. / Nicholls, R.A. / Atack, J.R. / Bax, B.D.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 4, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Serine racemase
BBB: Serine racemase
CCC: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,20340
Polymers150,7364
Non-polymers2,46736
Water14,268792
1
AAA: Serine racemase
CCC: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,93524
Polymers75,3682
Non-polymers1,56722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,26816
Polymers75,3682
Non-polymers90014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.062, 154.998, 85.652
Angle α, β, γ (deg.)90.000, 98.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase


Mass: 37683.977 Da / Num. of mol.: 4 / Mutation: C2D C6D
Source method: isolated from a genetically manipulated source
Details: Cofactor pyridoxal 5'-phosphate (PLP, LLP) is covalently bound to Lys56
Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus (DE3)-RIL
References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase

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Non-polymers , 8 types, 828 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: 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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Details

Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 mM MES pH 6.2 100 mM calcium chloride 5% ethylene glycol 20% PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.8→84.764 Å / Num. obs: 111815 / % possible obs: 97.8 % / Redundancy: 3.41 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 9.46
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 5444 / CC1/2: 0.651 / Rpim(I) all: 0.436 / Rrim(I) all: 0.829 / % possible all: 95.61

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SLH

6slh


Resolution: 1.8→84.764 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.173 / SU B: 5.551 / SU ML: 0.1 / Average fsc free: 0.9068 / Average fsc work: 0.9203 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2198 5508 4.932 %
Rwork0.1789 106173 -
all0.181 --
obs-111681 97.639 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å20 Å20.528 Å2
2---0.247 Å20 Å2
3---0.079 Å2
Refinement stepCycle: LAST / Resolution: 1.8→84.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 136 792 10340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01210320
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.62814146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44951400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18124.425391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485151615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4981530
X-RAY DIFFRACTIONr_chiral_restr0.10.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027790
X-RAY DIFFRACTIONr_nbd_refined0.2330.25676
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2840
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2840.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_mcbond_it1.392.7075424
X-RAY DIFFRACTIONr_mcangle_it2.3254.046882
X-RAY DIFFRACTIONr_scbond_it1.6352.8614896
X-RAY DIFFRACTIONr_scangle_it2.5794.2227264
X-RAY DIFFRACTIONr_lrange_it9.43551.76252324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.2983850.28676980.28784810.8330.83495.30720.276
1.847-1.8970.3054090.25974810.26181810.8190.84696.4430.245
1.897-1.9520.2673890.23273770.23479990.8770.88697.08710.217
1.952-2.0120.2613650.21271420.21577980.8860.90696.26830.196
2.012-2.0780.2553530.21169620.21375400.8890.90597.01590.195
2.078-2.1510.2323710.19367390.19572390.9140.92798.2180.178
2.151-2.2320.2433590.18464890.18770270.9170.93397.45270.171
2.232-2.3230.2293250.18562560.18767810.9190.93697.05060.173
2.323-2.4270.2562860.18661160.18965460.9070.92797.80020.175
2.427-2.5450.2223170.18457600.18661990.9240.93598.03190.174
2.545-2.6830.2252890.17755400.17959220.9320.94598.42960.168
2.683-2.8450.2152660.17852470.1855910.940.94698.60490.169
2.845-3.0410.2112460.16849200.1752280.9370.95298.81410.162
3.041-3.2850.2192230.16646180.16948920.9330.95198.95750.163
3.285-3.5980.1852170.15942230.16145010.9560.95898.64470.159
3.598-4.0210.1862010.14738370.14940950.9540.96698.60810.15
4.021-4.6420.1731860.13933770.14135880.9610.96999.30320.146
4.642-5.6810.211530.16928720.17130550.9510.9699.0180.176
5.681-8.0160.2461090.222640.20223930.9450.95599.16420.207
8.016-84.7640.205590.17412550.17513250.9480.96799.16980.197
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)
11.1290.2717-0.02160.6960.06871.21980.06660.1260.0507-0.12470.0240.0009-0.02270.0047-0.09060.03840.01850.01610.09270.01480.0536-9.2835-16.351928.273
20.50160.03530.04540.34490.02230.31560.0354-0.0186-0.03260.01220.0052-0.04810.01110.0026-0.04060.00730.00760.01120.04970.01040.081110.1611-26.08642.1325
32.45070.8428-0.73481.04790.12430.40860.25020.0627-0.32580.5119-0.2555-0.27510.1278-0.14850.00530.3052-0.1779-0.09480.12510.02490.1006-17.1357-69.715687.4667
40.4432-0.0026-0.00181.08440.24160.61560.0058-0.02410.03740.01840.0308-0.19380.1149-0.0788-0.03660.0815-0.0003-0.00110.0249-0.00350.04235.5076-60.713979.3886
52.0098-1.2818-0.37361.6190.24760.07520.14440.21130.0858-0.2386-0.1176-0.0685-0.0036-0.0286-0.02680.14750.0583-0.03980.042-0.01110.030818.4197-67.138133.6368
60.40270.2102-0.11161.1459-0.3560.2480.00750.04060.07880.05880.04270.20780.03330.0103-0.05020.0652-0.00630.00130.02060.01270.0986-5.5048-57.93841.8294
71.32671.04260.47741.30670.14060.95340.53280.07380.23520.524-0.22690.29220.13110.1274-0.30590.2409-0.02530.12560.1628-0.03190.2299.661-19.43889.75
80.6044-0.0391-0.13080.3432-0.12090.63490.0238-0.025-0.0134-0.0072-0.00730.04680.0147-0.015-0.01640.0139-0.00370.0180.0853-0.01410.0384-10.4384-29.076575.8933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA77 - 150
2X-RAY DIFFRACTION2ALLAAA7 - 55
3X-RAY DIFFRACTION2ALLAAA157 - 295
4X-RAY DIFFRACTION2ALLAAA307 - 315
5X-RAY DIFFRACTION3ALLBBB77 - 150
6X-RAY DIFFRACTION4ALLBBB7 - 55
7X-RAY DIFFRACTION4ALLBBB157 - 295
8X-RAY DIFFRACTION4ALLBBB307 - 315
9X-RAY DIFFRACTION5ALLCCC77 - 150
10X-RAY DIFFRACTION6ALLCCC7 - 55
11X-RAY DIFFRACTION6ALLCCC157 - 295
12X-RAY DIFFRACTION6ALLCCC307 - 315
13X-RAY DIFFRACTION7ALLDDD77 - 150
14X-RAY DIFFRACTION8ALLDDD7 - 55
15X-RAY DIFFRACTION8ALLDDD157 - 295
16X-RAY DIFFRACTION8ALLDDD307 - 315

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