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- PDB-3l6b: X-ray crystal structure of human serine racemase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3l6b
TitleX-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor
ComponentsSerine racemase
KeywordsISOMERASE / pyridoxal phosphate / PLP / serine racemase
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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / : / PYRIDOXAL-5'-PHOSPHATE / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSmith, M.A. / Barker, J. / Mack, V. / Ebneth, A. / Moraes, I. / Felicetti, B. / Cesura, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding.
Authors: Smith, M.A. / Mack, V. / Ebneth, A. / Moraes, I. / Felicetti, B. / Wood, M. / Schonfeld, D. / Mather, O. / Cesura, A. / Barker, J.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8604
Polymers37,4561
Non-polymers4043
Water3,909217
1
A: Serine racemase
hetero molecules

A: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7208
Polymers74,9122
Non-polymers8086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.570, 84.290, 69.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serine racemase


Mass: 37455.863 Da / Num. of mol.: 1 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZT4, serine racemase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008 / Details: MIRROR
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→38.32 Å / Num. obs: 52035 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.4 / Num. unique all: 49358 / Rsym value: 0.275 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD

Resolution: 1.5→36.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.248 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.5 / ESU R: 0.08 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2649 5.1 %RANDOM
Rwork0.16 ---
all0.161 49358 --
obs0.161 49358 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 23 217 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222507
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9813416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2635324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29725.48493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.949159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021842
X-RAY DIFFRACTIONr_nbd_refined0.2070.21269
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.29
X-RAY DIFFRACTIONr_mcbond_it0.9651.51656
X-RAY DIFFRACTIONr_mcangle_it1.52522618
X-RAY DIFFRACTIONr_scbond_it2.183958
X-RAY DIFFRACTIONr_scangle_it3.174.5796
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 193 -
Rwork0.208 3636 -
obs--99.97 %
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)
10.9839-0.19140.00550.896-0.25180.639-0.015-0.12090.03320.06580.0118-0.00520.00270.02260.00320.0781-0.0069-0.00270.0865-0.00970.0519-1.12228.432-10.028
221.9736-4.17490.90050.7932-0.17110.03690.0174-0.8719-0.55260.26990.3803-1.49760.85180.5373-0.39780.47920.0018-0.00050.47650.00530.480619.42714.511-9.61
31.9682-0.03980.20461.54810.21381.56620.005-0.02940.055-0.0221-0.0357-0.1477-0.02330.12960.03070.06450.00910.02180.06640.01120.08312.60921.876-23.606
42.08290.3986-0.18062.5257-0.16491.10090.00380.0559-0.0551-0.09540.0069-0.01180.07870.0651-0.01070.09210.01520.03020.0768-0.00160.067310.81416.816-29.589
50.7062-0.0954-0.14990.50790.02450.583-0.0092-0.0726-0.07250.01320.00960.05590.0477-0.0138-0.00040.0741-0.00560.00150.06150.01740.0698-5.62619.131-14.627
60.56150.02740.06330.6240.09620.4009-0.00640.011-0.0109-0.06370.00680.07370.0198-0.03-0.00040.0694-0.0059-0.00540.05920.00630.0723-8.93225.947-23.729
72.83730.0675-0.51291.12450.13170.7465-0.02060.0550.1314-0.01670.05360.1707-0.0158-0.1416-0.0330.07960.003-0.00390.0670.01710.0842-13.86331.172-16.971
80000000.0120.1840.6114-0.1565-0.00550.7892-0.5558-0.2247-0.00650.81290.00750.00180.81580.00120.8199-5.1439.245-35.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 64
2X-RAY DIFFRACTION2A65 - 76
3X-RAY DIFFRACTION3A77 - 115
4X-RAY DIFFRACTION4A116 - 143
5X-RAY DIFFRACTION5A144 - 229
6X-RAY DIFFRACTION6A230 - 295
7X-RAY DIFFRACTION7A296 - 319
8X-RAY DIFFRACTION8A320 - 329

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