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- PDB-3hmk: Crystal Structure of Serine Racemase -

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Basic information

Entry
Database: PDB / ID: 3hmk
TitleCrystal Structure of Serine Racemase
ComponentsSerine racemase
KeywordsISOMERASE / Serine Racemase / D-serine / pyridoxal phosphate / PLP / NMDA glutamate receptor / schizophrenia
Function / homology
Function and homology information


Serine metabolism / response to ketamine / : / 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 ...Serine metabolism / response to ketamine / : / 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 / 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
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
: / PYRIDOXAL-5'-PHOSPHATE / Serine racemase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSmith, M.A. / Barker, J. / Mack, V. / Ebneth, A. / Felicetti, B. / Woods, M.
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
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Nov 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Nov 1, 2023Group: 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
B: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7646
Polymers73,1592
Non-polymers6044
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.261, 102.960, 120.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine racemase


Mass: 36579.703 Da / Num. of mol.: 2 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Srr / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q76EQ0, serine racemase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2008
RadiationMonochromator: Double Crystal Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→41.1 Å / Num. all: 34466 / Num. obs: 32657 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.17 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1837 / Rsym value: 0.195 / % possible all: 74.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FKP

1fkp


Resolution: 2.1→41.1 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.637 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.336 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28949 1795 5.2 %RANDOM
Rwork0.24136 ---
obs0.24389 32657 95.77 %-
all-34466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.478 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 32 202 5078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224971
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.986775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29725.926189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35415827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1521514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213670
X-RAY DIFFRACTIONr_mcbond_it0.4021.53205
X-RAY DIFFRACTIONr_mcangle_it0.73925204
X-RAY DIFFRACTIONr_scbond_it0.77131766
X-RAY DIFFRACTIONr_scangle_it1.344.51571
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 99 -
Rwork0.288 1786 -
obs--73.12 %

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