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- PDB-3l6r: The structure of mammalian serine racemase: Evidence for conforma... -

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Basic information

Entry
Database: PDB / ID: 3l6r
TitleThe structure of mammalian serine racemase: Evidence for conformational changes upon inhibitor binding
ComponentsSerine racemase
KeywordsISOMERASE / pyridoxal phosphate / PLP / serine racemase
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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / : / Serine racemase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSmith, M.A. / Mack, V. / Ebneth, A. / Cesura, A. / Felicetti, B. / Barker, J.
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 24, 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0753
Polymers37,9181
Non-polymers1572
Water6,359353
1
A: Serine racemase
hetero molecules

A: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1516
Polymers75,8372
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1710 Å2
ΔGint-17 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.543, 84.212, 70.376
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: 37918.449 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: pET 24A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZT4, serine racemase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, 200mM sodium malonate, 50mM MnCl2, 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: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2008
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→45.78 Å / Num. all: 35305 / Num. obs: 35305 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.45 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.097 / Net I/σ(I): 16.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.44 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.31 / % possible all: 78.9

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→45.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.169 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1775 5 %RANDOM
Rwork0.1676 ---
obs-33537 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 8 353 2788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222549
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.9843491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26825.69993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70715441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.399158
X-RAY DIFFRACTIONr_chiral_restr0.1540.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211869
X-RAY DIFFRACTIONr_mcbond_it2.0731.51632
X-RAY DIFFRACTIONr_mcangle_it3.27322668
X-RAY DIFFRACTIONr_scbond_it4.7553917
X-RAY DIFFRACTIONr_scangle_it7.2844.5812
X-RAY DIFFRACTIONr_rigid_bond_restr2.58932549
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 91 -
Rwork0.2 1925 -
obs--76.54 %
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)
10.3762-0.0362-0.01760.2186-0.13370.1332-0.0069-0.05050.00920.00830.0129-0.00060.00430.0012-0.0060.06260.0012-0.00150.066-0.00030.0495-1.122428.4318-10.0281
230.83492.0734-5.310614.8012-14.417314.4014-2.6765-2.4847-1.32050.6610.4773-2.0827-0.3171-0.1342.19920.46770.3125-0.01270.38010.02040.347219.426814.511-9.6096
30.647-0.1051-0.13910.47230.0020.59720.0264-0.02150.0219-0.0053-0.0201-0.0503-0.01720.0502-0.00620.0578-0.00040.00620.0591-0.00010.059712.609321.8763-23.6062
40.82420.0721-0.45740.48310.11980.5461-0.0132-0.0018-0.0026-0.02660.01020.01960.02140.03550.0030.06380.00540.00440.05460.00020.052510.813916.8157-29.5889
50.2251-0.0854-0.05340.1955-0.10690.31090.0038-0.0341-0.0313-0.00340.00420.02010.0206-0.0083-0.0080.0616-0.0030.00050.06050.00520.0542-5.625519.131-14.6274
60.24510.04480.06020.18130.00480.1629-0.00380.0016-0.0042-0.02210.00370.02090.0085-0.00940.00010.0618-0.0024-0.00070.0580.0040.0533-8.932325.9465-23.7286
71.31020.0228-0.63690.4161-0.15840.4662-0.02280.02080.0363-0.00360.03660.0496-0.0016-0.0433-0.01380.06070.00050.00090.06510.00490.0593-13.862931.1723-16.971
87.2982-8.1532-2.77099.99130.56258.31960.48950.2998-0.4593-0.5384-0.65110.5154-0.24320.7730.16150.1522-0.0382-0.06970.1436-0.0010.0556-5.139939.2453-35.9661
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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