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- PDB-7nbf: Crystal structure of human serine racemase in complex with DSiP f... -

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Basic information

Entry
Database: PDB / ID: 7nbf
TitleCrystal structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen.
ComponentsSerine racemase
KeywordsISOMERASE / Racemase / XChem / Inhibitor
Function / homology
Function and homology information


D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / serine family amino acid metabolic process / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine metabolic process ...D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / serine family amino acid metabolic process / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine metabolic process / Serine metabolism / pyruvate biosynthetic process / L-serine metabolic process / glycine binding / PDZ domain binding / : / 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 / cytosol / cytoplasm
Similarity search - Function
Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / 2-[(methylsulfonyl)methyl]-1H-benzimidazole / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKoulouris, C.R. / Roe, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
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
DepositionJan 26, 2021Deposition 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)153,47242
Polymers149,8234
Non-polymers3,64938
Water16,574920
1
AAA: Serine racemase
CCC: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,96522
Polymers74,9122
Non-polymers2,05320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-64 kcal/mol
Surface area25260 Å2
MethodPISA
2
BBB: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,50820
Polymers74,9122
Non-polymers1,59618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-85 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.112, 154.937, 85.539
Angle α, β, γ (deg.)90.000, 97.957, 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: 37455.863 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 lysine 56
Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (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 , 11 types, 958 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P
Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-T6J / 2-[(methylsulfonyl)methyl]-1H-benzimidazole


Mass: 210.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H10N2O2S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.7 %
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 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.599→84.716 Å / Num. obs: 158956 / % possible obs: 97.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.082 / Net I/σ(I): 8.9
Reflection shellResolution: 1.599→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7536 / CC1/2: 0.383 / Rrim(I) all: 0.889 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZUJ

6zuj


Resolution: 1.6→84.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.547 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.089 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1982 7962 5.012 %
Rwork0.1722 150883 -
all0.173 --
obs-158845 97.468 %
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: 28.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.112 Å2
2--0.195 Å20 Å2
3----0.112 Å2
Refinement stepCycle: LAST / Resolution: 1.6→84.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9445 0 218 920 10583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01210627
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.62814602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23351429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04624.723415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.963151680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9481530
X-RAY DIFFRACTIONr_chiral_restr0.1270.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028046
X-RAY DIFFRACTIONr_nbd_refined0.2220.25577
X-RAY DIFFRACTIONr_nbtor_refined0.3170.27066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2805
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.231
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3130.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_mcbond_it2.0022.2465517
X-RAY DIFFRACTIONr_mcangle_it3.1093.3427013
X-RAY DIFFRACTIONr_scbond_it2.8792.4955110
X-RAY DIFFRACTIONr_scangle_it4.3023.6477589
X-RAY DIFFRACTIONr_lrange_it10.17744.04453708
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
1.599-1.6410.3356000.303107190.305120180.6980.72494.18370.295
1.641-1.6860.2835700.29107130.289117040.750.7696.40290.277
1.686-1.7350.2765160.265105270.265114230.830.83896.67340.249
1.735-1.7880.2795300.246102070.248111010.850.86296.7210.226
1.788-1.8470.2385290.21699030.217107500.8950.90297.04190.193
1.847-1.9110.2195020.1995500.191103420.9220.92697.19590.167
1.911-1.9830.214930.17792520.17899970.9320.93697.47920.157
1.983-2.0640.2074550.17689580.17796450.9390.94397.59460.159
2.064-2.1560.1944690.16685880.16892570.9440.95197.83950.151
2.156-2.2610.1924320.16282340.16388530.9480.95697.88770.147
2.261-2.3830.1894570.15478270.15684360.9520.96198.19820.143
2.383-2.5280.1853690.15174660.15379800.9520.9698.1830.141
2.528-2.7020.1973590.15869920.1674650.9460.95798.47290.15
2.702-2.9190.1923300.15565410.15769630.9520.96198.67870.148
2.919-3.1970.1853450.15360300.15564380.9560.96199.02140.15
3.197-3.5730.1922890.1554650.15258060.9510.96599.10440.151
3.573-4.1250.1462640.13748220.13751250.9750.97699.2390.143
4.125-5.0490.1512050.13941220.1443520.9710.97599.42560.15
5.049-7.1280.2411680.231800.20233830.9450.95798.96540.209
7.128-84.7160.177800.20917880.20718820.9670.96799.25610.232
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)
10.4609-0.7891-0.77471.51370.70964.06890.196-0.00880.0348-0.3713-0.01220.0113-0.15610.2099-0.18380.09520.01160.01340.06020.02260.0823-8.8145-14.507125.2393
20.31740.0290.00010.40560.06180.25330.0188-0.0113-0.02130.02150.0084-0.05460.0151-0.0049-0.02720.01580.00430.0150.02940.01050.059710.4142-25.917942.2364
33.17281.5691-0.63442.2029-0.11790.15370.3275-0.2319-0.1750.6765-0.37960.0480.00480.01020.05210.2201-0.11570.03460.07640.00250.042-16.0314-69.956788.035
40.2516-0.1811-0.08410.91820.03590.2687-0.0229-0.00750.04540.01610.0295-0.12070.036-0.0294-0.00670.04560.0090.00540.02280.00610.02536.047-60.703579.3113
50.6597-0.95840.47682.042-0.34531.39440.06480.05960.0222-0.2383-0.1084-0.14290.0409-0.01870.04360.11520.02990.02060.0167-0.00370.030819.9392-68.89130.1376
60.45440.1962-0.06530.7472-0.22910.1686-0.01860.03620.07520.02710.0490.10210.0519-0.0051-0.03040.0714-0.00620.00990.01120.00880.0335-5.1981-57.819341.6482
70.08020.3156-0.35094.63411.09173.99370.0464-0.00650.03380.8866-0.24750.30840.4046-0.06230.20110.2198-0.0740.12220.0566-0.02590.13510.074-17.549893.0297
80.5225-0.037-0.00490.3309-0.11240.44890.0227-0.0068-0.0190.0005-0.00860.0460.0116-0.0126-0.01410.02-0.00210.02030.0558-0.01170.0315-10.0238-29.11675.8884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA101 - 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 DIFFRACTION5ALLCCC101 - 150
10X-RAY DIFFRACTION6ALLCCC7 - 55
11X-RAY DIFFRACTION6ALLCCC157 - 295
12X-RAY DIFFRACTION6ALLCCC307 - 315
13X-RAY DIFFRACTION7ALLDDD101 - 150
14X-RAY DIFFRACTION8ALLDDD7 - 55
15X-RAY DIFFRACTION8ALLDDD157 - 295
16X-RAY DIFFRACTION8ALLDDD307 - 315

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