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- PDB-5fac: Alanine Racemase from Streptomyces coelicolor A3(2) -

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Basic information

Entry
Database: PDB / ID: 5fac
TitleAlanine Racemase from Streptomyces coelicolor A3(2)
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
PYRIDOXAL-5'-PHOSPHATE / Alanine racemase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)174,62612
Polymers173,4964
Non-polymers1,1308
Water3,081171
1
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3136
Polymers86,7482
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-35 kcal/mol
Surface area25580 Å2
MethodPISA
2
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3136
Polymers86,7482
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-36 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.960, 87.170, 109.626
Angle α, β, γ (deg.)90.00, 102.26, 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: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA11 - 39030 - 409
21ASNASNBB11 - 39030 - 409
12ASNASNAA9 - 39028 - 409
22ASNASNCC9 - 39028 - 409
13ASNASNAA11 - 39030 - 409
23ASNASNDD11 - 39030 - 409
14ASNASNBB11 - 39030 - 409
24ASNASNCC11 - 39030 - 409
15GLUGLUBB11 - 39130 - 410
25GLUGLUDD11 - 39130 - 410
16ASNASNCC11 - 39030 - 409
26ASNASNDD11 - 39030 - 409

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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O86786, alanine racemase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.12 Å3/Da / Density % sol: 42.12 %
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: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.8→47.78 Å / Num. obs: 32860 / % possible obs: 95.96 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 3.8
Reflection shellResolution: 2.8→2.94 Å / Mean I/σ(I) obs: 1.3 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VFH

1vfh


Resolution: 2.8→47.78 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 22.747 / SU ML: 0.416 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25918 1693 4.9 %RANDOM
Rwork0.20847 ---
obs0.211 32860 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.888 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-1 Å2
2--5.96 Å20 Å2
3----3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11337 0 64 171 11572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911704
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211087
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.96715985
X-RAY DIFFRACTIONr_angle_other_deg1.393325387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42351531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5121.799478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.84515132
X-RAY DIFFRACTIONr_chiral_restr0.0830.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113476
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022648
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_it3.0814.3656118
X-RAY DIFFRACTIONr_mcbond_other3.0814.3656117
X-RAY DIFFRACTIONr_mcangle_it4.9716.5427642
X-RAY DIFFRACTIONr_mcangle_other4.9716.5427643
X-RAY DIFFRACTIONr_scbond_it3.294.7255586
X-RAY DIFFRACTIONr_scbond_other3.294.7255587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.386.9378341
X-RAY DIFFRACTIONr_long_range_B_refined8.39734.99812762
X-RAY DIFFRACTIONr_long_range_B_other8.39835.01312754
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)
11A439360.07
12B439360.07
21A438700.08
22C438700.08
31A440620.08
32D440620.08
41B442080.07
42C442080.07
51B446180.07
52D446180.07
61C442780.07
62D442780.07
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 107 -
Rwork0.355 2035 -
obs--81.38 %

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