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

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Basic information

Entry
Database: PDB / ID: 7nbg
TitleCrystal structure of human serine racemase in complex with DSiP fragment Z52314092, 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 / 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 / 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 / apical part of cell / pyridoxal phosphate binding / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
ORTHO-XYLENE / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / ~{N}-[2-(2-methylphenyl)ethyl]ethanamide / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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)153,38048
Polymers149,8234
Non-polymers3,55744
Water16,952941
1
AAA: Serine racemase
CCC: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,82027
Polymers74,9122
Non-polymers1,90925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Serine racemase
DDD: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,56021
Polymers74,9122
Non-polymers1,64819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.110, 154.760, 85.400
Angle α, β, γ (deg.)90.000, 98.140, 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 Lys56
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, 985 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 Lys56
References: serine racemase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-U78 / ~{N}-[2-(2-methylphenyl)ethyl]ethanamide


Mass: 177.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15NO / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
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 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.53→77.4 Å / Num. obs: 177718 / % possible obs: 95.9 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.075 / Net I/σ(I): 9
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.804 / Num. unique obs: 11899 / CC1/2: 0.453 / % possible all: 87

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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: 1.53→77.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.159 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.083 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.202 8706 4.9 %
Rwork0.1823 168961 -
all0.183 --
obs-177667 95.829 %
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: 28.092 Å2
Baniso -1Baniso -2Baniso -3
1--0.039 Å20 Å20.601 Å2
2---0.461 Å20 Å2
3---0.315 Å2
Refinement stepCycle: LAST / Resolution: 1.53→77.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9368 0 159 941 10468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01210883
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.62914968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07551488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71724.648426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.136151715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3521530
X-RAY DIFFRACTIONr_chiral_restr0.0870.21480
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028335
X-RAY DIFFRACTIONr_nbd_refined0.2140.25823
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2881
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.244
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_mcbond_it0.992.2735659
X-RAY DIFFRACTIONr_mcangle_it1.6993.3967244
X-RAY DIFFRACTIONr_scbond_it1.222.4475224
X-RAY DIFFRACTIONr_scangle_it1.9463.6067724
X-RAY DIFFRACTIONr_lrange_it8.23844.31354374
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
1.53-1.570.325790.312113100.312136810.7110.71386.90150.314
1.57-1.6130.3046330.292113490.293133990.7940.80189.42460.289
1.613-1.6590.2876170.269118130.269129570.8430.8595.93270.259
1.659-1.7110.2625940.25114910.251125760.8730.87896.09570.237
1.711-1.7670.2525510.23111830.231122000.8920.90596.18030.214
1.767-1.8290.2356240.208107320.21117900.920.92296.31890.192
1.829-1.8980.2275240.19105660.192114420.9250.93596.92360.174
1.898-1.9750.2145320.183100790.185109590.9320.94496.82450.17
1.975-2.0630.1955050.18397120.183105110.9520.95397.20290.172
2.063-2.1630.194670.17793240.178100830.9550.95897.1040.17
2.163-2.280.2054280.17589330.17795930.9460.95597.58160.168
2.28-2.4180.2024250.1784430.17290840.9480.95797.62220.168
2.418-2.5850.1863550.16979580.1785030.950.95997.76550.17
2.585-2.7920.2053650.17274020.17479300.9460.95797.94450.177
2.792-3.0580.1963770.17268050.17373210.9510.95698.10140.183
3.058-3.4190.1823280.16361830.16466150.960.96398.42780.18
3.419-3.9460.1762790.15554330.15658170.9610.96698.19490.177
3.946-4.830.1612430.14446310.14549590.9660.97198.28590.175
4.83-6.8170.2151740.20636080.20738400.940.94898.48960.25
6.817-77.380.1911060.19920050.19821400.9630.96298.64490.258
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)
10.7494-0.048-0.13060.2990.0171.04090.10420.01070.0952-0.1274-0.0070.02750.0575-0.0073-0.09710.07250.0142-0.00250.04250.01440.0326-9.2686-16.463728.2787
20.24160.0519-0.01280.36180.08530.21310.028-0.0073-0.01530.01860.0049-0.06190.0124-0.0139-0.03290.00530.0020.00010.03460.0120.041310.351-25.869542.1118
31.24240.674-0.44450.77580.10780.52680.11220.0334-0.05280.2525-0.0471-0.05410.0718-0.0566-0.06510.13-0.02870.02230.0145-0.00130.0521-16.1444-70.029687.7696
40.2802-0.0913-0.0420.68140.05340.13690.0073-0.00240.04230.00960.0027-0.09760.0266-0.0157-0.010.0380.02020.00170.0260.00310.01835.8802-60.831179.0788
50.452-0.5210.01980.83250.15570.26650.09860.04790.0224-0.1068-0.0528-0.03030.00620.004-0.04580.06290.0209-0.00320.01950.00270.018418.8353-66.933633.1412
60.37930.0802-0.03750.4658-0.21470.11650.00020.01380.05940.00140.02620.06190.0279-0.007-0.02640.0586-0.0047-0.00120.01580.00910.0161-5.3138-57.879641.5204
71.30070.92320.82111.12070.33780.70230.3534-0.05770.07240.3915-0.24740.20030.13850.0601-0.1060.1446-0.07170.08420.0898-0.05660.132610.2506-19.610889.4176
80.3369-0.0901-0.04660.3065-0.1230.40.0194-0.0027-0.0175-0.0032-0.01170.04050.0094-0.007-0.00780.0047-0.00130.00520.0505-0.0120.0181-10.1868-29.135875.7896
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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