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- PDB-5fag: Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Pr... -

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Basic information

Entry
Database: PDB / ID: 5fag
TitleAlanine Racemase from Streptomyces coelicolor A3(2) with Bound Propionate Inhibitor
ComponentsAlanine racemase
KeywordsISOMERASE / PLP / alanine racemase / propionate
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
NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / PROPANOIC ACID / Alanine racemase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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_conn_type / 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_conn_type.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)175,31623
Polymers173,4964
Non-polymers1,82019
Water14,484804
1
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,82915
Polymers86,7482
Non-polymers1,08113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-46 kcal/mol
Surface area25700 Å2
MethodPISA
2
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4878
Polymers86,7482
Non-polymers7406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint2 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.950, 88.580, 108.880
Angle α, β, γ (deg.)90.00, 102.60, 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

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 823 molecules

#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-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS propane pH 8.5, 0.2 M NaNO3, 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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968622 Å / Relative weight: 1
ReflectionResolution: 1.51→48.06 Å / Num. obs: 224162 / % possible obs: 96.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.3
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 0.8 / % possible all: 90.4

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Processing

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

5fac


Resolution: 1.51→48.06 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.783 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22528 11051 4.9 %RANDOM
Rwork0.19865 ---
obs0.19998 212779 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.274 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0.64 Å2
2--2.34 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.51→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11384 0 113 804 12301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912235
X-RAY DIFFRACTIONr_bond_other_d0.0110.0211706
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.97116775
X-RAY DIFFRACTIONr_angle_other_deg1.755326845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90251659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45321.44521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.811151795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1815159
X-RAY DIFFRACTIONr_chiral_restr0.1210.21838
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02114200
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022827
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_it3.1343.0266271
X-RAY DIFFRACTIONr_mcbond_other3.1343.0266270
X-RAY DIFFRACTIONr_mcangle_it4.0224.5327865
X-RAY DIFFRACTIONr_mcangle_other4.0224.5327866
X-RAY DIFFRACTIONr_scbond_it3.7783.4055964
X-RAY DIFFRACTIONr_scbond_other3.7773.4045959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4134.9648842
X-RAY DIFFRACTIONr_long_range_B_refined6.625.06514362
X-RAY DIFFRACTIONr_long_range_B_other6.60225.06714363
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)
11A463560.08
12B463560.08
21A462140.08
22C462140.08
31A459900.07
32D459900.07
41B461240.07
42C461240.07
51B457260.07
52D457260.07
61C459880.07
62D459880.07
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 697 -
Rwork0.421 14019 -
obs--86.34 %

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