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- PDB-5faj: Alanine Racemase from Streptomyces coelicolor A3(2) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5faj
TitleAlanine Racemase from Streptomyces coelicolor A3(2) in complex with D-Cycloserine
ComponentsAlanine racemase
KeywordsISOMERASE / PLP / alanine racemase
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DCS / Alanine racemase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTassoni, R. / Pannu, N.S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2).
Authors: Tassoni, R. / van der Aart, L.T. / Ubbink, M. / van Wezel, G.P. / Pannu, N.S.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,14419
Polymers173,4964
Non-polymers1,64815
Water13,691760
1
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5679
Polymers86,7482
Non-polymers8197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-72 kcal/mol
Surface area25450 Å2
MethodPISA
2
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57710
Polymers86,7482
Non-polymers8298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-73 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.740, 88.710, 109.140
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA10 - 39029 - 409
21ASNASNBB10 - 39029 - 409
12ASNASNAA10 - 39029 - 409
22ASNASNCC10 - 39029 - 409
13ASNASNAA10 - 39029 - 409
23ASNASNDD10 - 39029 - 409
14GLUGLUBB10 - 39129 - 410
24GLUGLUCC10 - 39129 - 410
15GLUGLUBB10 - 39129 - 410
25GLUGLUDD10 - 39129 - 410
16GLUGLUCC10 - 39129 - 410
26GLUGLUDD10 - 39129 - 410

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alanine racemase /


Mass: 43373.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: alr, SCO4745, SC6G4.23 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O86786, alanine racemase
#2: Chemical
ChemComp-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N3O7P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS propane pH 8.5, 0.2 M NaBr, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.968622 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968622 Å / Relative weight: 1
ReflectionResolution: 1.64→49.13 Å / Num. obs: 177142 / % possible obs: 97.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.4
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 0.6 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAC

5fac


Resolution: 1.64→106.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.414 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 6996 5 %RANDOM
Rwork0.20782 ---
obs0.20948 133358 77.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.731 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.03 Å2
2--0.13 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.64→106.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11350 0 99 760 12209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911845
X-RAY DIFFRACTIONr_bond_other_d0.0090.0211271
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9716192
X-RAY DIFFRACTIONr_angle_other_deg1.598325812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19351557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75821.557488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.918151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.07115142
X-RAY DIFFRACTIONr_chiral_restr0.1090.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113664
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022710
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_it3.1123.0926162
X-RAY DIFFRACTIONr_mcbond_other3.1113.0936162
X-RAY DIFFRACTIONr_mcangle_it4.3054.6257696
X-RAY DIFFRACTIONr_mcangle_other4.3054.6267697
X-RAY DIFFRACTIONr_scbond_it3.583.455683
X-RAY DIFFRACTIONr_scbond_other3.5793.455679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2815.0468476
X-RAY DIFFRACTIONr_long_range_B_refined6.98225.5313798
X-RAY DIFFRACTIONr_long_range_B_other6.97325.41313497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A456540.06
12B456540.06
21A456260.07
22C456260.07
31A456180.07
32D456180.07
41B460640.06
42C460640.06
51B456680.07
52D456680.07
61C458580.06
62D458580.06
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 65 -
Rwork0.547 1081 -
obs--8.56 %

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