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- PDB-5cvc: Structure of maize serine racemase -

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Basic information

Entry
Database: PDB / ID: 5cvc
TitleStructure of maize serine racemase
ComponentsSerine racemase
KeywordsISOMERASE / maize serine racemase
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
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 speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSong, Y. / Zou, L. / Fan, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of maize serine racemase with pyridoxal 5'-phosphate.
Authors: Zou, L. / Song, Y. / Wang, C. / Sun, J. / Wang, L. / Cheng, B. / Fan, J.
History
DepositionJul 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Advisory / Derived calculations
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _pdbx_struct_oper_list.symmetry_operation / _struct_site.details ..._pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine racemase
B: Serine racemase
C: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0649
Polymers110,2493
Non-polymers8146
Water3,531196
1
A: Serine racemase
C: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0426
Polymers73,5002
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-48 kcal/mol
Surface area23470 Å2
MethodPISA
2
B: Serine racemase
hetero molecules

B: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0426
Polymers73,5002
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3810 Å2
ΔGint-45 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.992, 204.017, 211.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine racemase


Mass: 36749.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: F5CAQ9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 64417 / % possible obs: 98.9 % / Redundancy: 5.5 % / Net I/σ(I): 17.82

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
MrBUMPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HMK

3hmk


Resolution: 2.09→41.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.231 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22868 3283 5.1 %RANDOM
Rwork0.19805 ---
obs0.19966 61516 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: 32.296 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--0.66 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.09→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6991 0 48 196 7235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197192
X-RAY DIFFRACTIONr_bond_other_d0.0050.026912
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9619800
X-RAY DIFFRACTIONr_angle_other_deg0.814315861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92524.426235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7931525
X-RAY DIFFRACTIONr_chiral_restr0.080.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5273.223867
X-RAY DIFFRACTIONr_mcbond_other1.5273.2193866
X-RAY DIFFRACTIONr_mcangle_it2.324.8134825
X-RAY DIFFRACTIONr_mcangle_other2.3194.8144826
X-RAY DIFFRACTIONr_scbond_it1.9093.4373325
X-RAY DIFFRACTIONr_scbond_other1.9083.4373326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9385.0814976
X-RAY DIFFRACTIONr_long_range_B_refined4.1726.3948222
X-RAY DIFFRACTIONr_long_range_B_other4.1726.3948223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 248 -
Rwork0.238 4363 -
obs--96.02 %

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