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- PDB-6zsp: Human serine racemase bound to ATP and malonate. -

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Basic information

Entry
Database: PDB / ID: 6zsp
TitleHuman serine racemase bound to ATP and malonate.
ComponentsSerine racemase
KeywordsISOMERASE / PLP-dependent / D-serine / ATP / forebrain
Function / homology
Function and homology information


D-serine biosynthetic process / serine racemase / threonine racemase activity / 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 ...D-serine biosynthetic process / serine racemase / threonine racemase activity / 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
ADENOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / MALONATE ION / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,56619
Polymers75,6242
Non-polymers1,94117
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration markers indicated the molecular weight of the macromolecule was over 70 kDa thus suggesting the protein is dimeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-32 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.943, 81.191, 134.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AAABBB

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


Mass: 37812.105 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase

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Non-polymers , 7 types, 385 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350 230 mM sodium malonate 15 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50.1 Å / Num. obs: 76688 / % possible obs: 97.5 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.079 / Net I/σ(I): 9.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3151 / CC1/2: 0.512 / Rrim(I) all: 0.705 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L6B

3l6b


Resolution: 1.6→42.651 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.173 / SU B: 4.308 / SU ML: 0.082 / Average fsc free: 0.8878 / Average fsc work: 0.8966 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.226 3722 4.927 %
Rwork0.1923 71820 -
all0.194 --
obs-75542 96.017 %
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: 21.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.556 Å20 Å20 Å2
2--0.546 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 121 368 5289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125635
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.6347761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03324.429219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41615931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2121517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024282
X-RAY DIFFRACTIONr_nbd_refined0.2280.23035
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2403
X-RAY DIFFRACTIONr_metal_ion_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.222
X-RAY DIFFRACTIONr_mcbond_it0.9921.6592867
X-RAY DIFFRACTIONr_mcangle_it1.6892.4773672
X-RAY DIFFRACTIONr_scbond_it1.1681.8152768
X-RAY DIFFRACTIONr_scangle_it1.9272.6664084
X-RAY DIFFRACTIONr_lrange_it5.2131.22824760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.4382150.3934368X-RAY DIFFRACTION80.0664
1.642-1.6870.3772510.3594944X-RAY DIFFRACTION92.1426
1.687-1.7350.332430.3314892X-RAY DIFFRACTION95.0222
1.735-1.7890.312620.2934807X-RAY DIFFRACTION95.7318
1.789-1.8470.2922500.2664734X-RAY DIFFRACTION96.7767
1.847-1.9120.2492450.2384582X-RAY DIFFRACTION97.1032
1.912-1.9840.2442460.2144460X-RAY DIFFRACTION97.8175
1.984-2.0650.2672170.2014285X-RAY DIFFRACTION97.467
2.065-2.1570.2072210.1824169X-RAY DIFFRACTION98.4305
2.157-2.2620.2141840.174003X-RAY DIFFRACTION98.2633
2.262-2.3840.2071940.1683783X-RAY DIFFRACTION98.1733
2.384-2.5280.1981920.1673603X-RAY DIFFRACTION98.8281
2.528-2.7020.2011710.1623432X-RAY DIFFRACTION98.5773
2.702-2.9180.2021750.1623152X-RAY DIFFRACTION99.0768
2.918-3.1950.1831570.1532962X-RAY DIFFRACTION99.2048
3.195-3.5710.2231490.1532655X-RAY DIFFRACTION98.4896
3.571-4.1190.1921180.1482393X-RAY DIFFRACTION99.2098
4.119-5.0370.1731150.1462043X-RAY DIFFRACTION99.3554
5.037-7.0870.187720.1851615X-RAY DIFFRACTION98.8284
7.087-42.650.196450.203939X-RAY DIFFRACTION94.9807
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)
10.67040.21090.33190.7329-0.12570.674-0.04290.00970.0811-0.0440.04040.1538-0.0254-0.00350.00250.01950.008-0.02140.03240.0240.06431.2024-6.2773-23.6448
20.48960.0071-0.07810.97360.09180.0663-0.01960.02090.0160.07880.0097-0.14580.0024-0.00870.00990.021-0.0072-0.02520.01050.00110.041920.9561-13.0423-14.5453
31.5651-0.0272-0.46110.75830.46660.5895-0.040.05220.02580.0090.0228-0.07240.07270.0330.01710.02190.01640.01630.0291-0.00450.049525.7124-52.7461-24.299
40.7125-0.3531-0.09260.59470.09450.1378-0.0689-0.011-0.0620.05110.01120.10220.01050.01260.05760.0231-0.00250.01610.0151-0.00050.03585.8097-46.3174-15.2475
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

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