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- PDB-6g56: Apo-structure of the alanine racemase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6g56
TitleApo-structure of the alanine racemase from Staphylococcus aureus
ComponentsAlanine racemase 1
KeywordsBIOSYNTHETIC PROTEIN / pyridoxal 5 phosphate dependent / D-alanine biosynthesis
Function / homologyAlanine racemase / Alanine racemase, N-terminal / Alanine racemase/group IV decarboxylase, C-terminal / Alanine racemase, C-terminal / Alanine racemase, pyridoxal-phosphate attachment site / PLP-binding barrel / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal domain / Alanine racemase pyridoxal-phosphate attachment site. / D-alanine biosynthetic process ...Alanine racemase / Alanine racemase, N-terminal / Alanine racemase/group IV decarboxylase, C-terminal / Alanine racemase, C-terminal / Alanine racemase, pyridoxal-phosphate attachment site / PLP-binding barrel / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal domain / Alanine racemase pyridoxal-phosphate attachment site. / D-alanine biosynthetic process / alanine racemase / alanine racemase activity / pyridoxal phosphate binding / Alanine racemase 1
Function and homology information
Specimen sourceStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.15 Å resolution
AuthorsHoegl, A. / Sieber, S.A. / Schneider, S.
Funding supportGermany , 2 items
OrganizationGrant numberCountry
European Research Council725085Germany
German Research FoundationEXC 114Germany
CitationJournal: Nat Chem / Year: 2018
Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.
Authors: Hoegl, A. / Nodwell, M.B. / Kirsch, V.C. / Bach, N.C. / Pfanzelt, M. / Stahl, M. / Schneider, S. / Sieber, S.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2018 / Release: May 30, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 30, 2018Structure modelrepositoryInitial release
1.1Oct 17, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
1.2Dec 5, 2018Structure modelData collection / Database referencescitation / citation_author / pdbx_database_proc_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanine racemase 1
B: Alanine racemase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,15329
Polyers90,5722
Non-polymers2,58227
Water5,350297
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11570
ΔGint (kcal/M)-346
Surface area (Å2)27600
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)64.701, 114.521, 126.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide Alanine racemase 1 /


Mass: 45285.801 Da / Num. of mol.: 2 / Details: N-terminal Strep-tag
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Gene: alr1, alr, SAV2070 / Production host: Escherichia coli (E. coli) / References: UniProt: P63479, alanine racemase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Formula: SO4 / Sulfate
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Formula: H2O / Water

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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: 2.58 / Density percent sol: 52.31 %
Crystal growTemp: 277 K / Method: vapor diffusion, sitting drop / Details: 2M Ammonium sulphate, 50mM Sodium acetate, pH 6

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: Apr 8, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 34.4 Å2 / D resolution high: 2.15 Å / D resolution low: 84.78 Å / Number obs: 51458 / CC half: 0.99 / Rmerge I obs: 0.166 / Rrim I all: 0.2 / NetI over sigmaI: 6 / Redundancy: 5.2 % / Percent possible obs: 100
Reflection shellRmerge I obs: 1.73 / Highest resolution: 2.15 Å / Lowest resolution: 2.2 Å / MeanI over sigI obs: 0.4 / Number unique obs: 4390 / CC half: 0.85 / Redundancy: 5.1 % / Percent possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A3Q
Correlation coeff Fo to Fc: 0.948 / Correlation coeff Fo to Fc free: 0.929 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 12.272 / Overall SU ML: 0.154 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.257 / Overall ESU R Free: 0.205
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1 Å
Displacement parametersB iso mean: 33.99 Å2 / Aniso B11: -0.6 Å2 / Aniso B12: - Å2 / Aniso B13: 0 Å2 / Aniso B22: 1.12 Å2 / Aniso B23: - Å2 / Aniso B33: -0.52 Å2
Least-squares processR factor R free: 0.25386 / R factor R work: 0.21685 / R factor obs: 0.21871 / Highest resolution: 2.15 Å / Lowest resolution: 84.78 Å / Number reflection R free: 2538 / Number reflection obs: 48216 / Percent reflection R free: 5 / Percent reflection obs: 98.1
Refine hist #1Highest resolution: 2.15 Å / Lowest resolution: 84.78 Å
Number of atoms included #1Protein: 6000 / Nucleic acid: 0 / Ligand: 138 / Solvent: 297 / Total: 6435
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196273
X-RAY DIFFRACTIONr_bond_other_d0.0020.0205774
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9738526
X-RAY DIFFRACTIONr_angle_other_deg0.9403.00013426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925.000777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49224.910279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90415.0001091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.64815.00028
X-RAY DIFFRACTIONr_chiral_restr0.0810.200988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0206857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0201183
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_it2.1611.3723072
X-RAY DIFFRACTIONr_mcbond_other2.1601.3723071
X-RAY DIFFRACTIONr_mcangle_it3.2712.0483843
X-RAY DIFFRACTIONr_mcangle_other3.2712.0493844
X-RAY DIFFRACTIONr_scbond_it4.2411.7513201
X-RAY DIFFRACTIONr_scbond_other4.2351.7513201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7042.5114678
X-RAY DIFFRACTIONr_long_range_B_refined7.79317.0096818
X-RAY DIFFRACTIONr_long_range_B_other7.78717.0096818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints ncs

Ens ID: 1 / Number: 24086 / Refine ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom IDAuth asym ID
1A
2B
Refine LS shellHighest resolution: 2.15 Å / R factor R free: 0.522 / R factor R work: 0.531 / Lowest resolution: 2.206 Å / Number reflection R free: 177 / Number reflection R work: 3359 / Total number of bins used: 20 / Percent reflection obs: 93.59
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.1362-0.0656-0.20460.34230.90753.3664-0.02700.07130.0618-0.03710.0973-0.0906-0.07280.2821-0.07030.18800.0014-0.00390.0693-0.00440.063712.6530-15.3560-46.1950
22.84710.28050.13971.80270.34261.92400.0040-0.03600.2352-0.0820-0.0799-0.1033-0.16140.09180.07590.1931-0.0065-0.00550.02830.00690.03272.1990-5.9860-54.7240
32.7448-0.91950.77664.1760-0.26482.2477-0.0580-0.00960.02490.02110.02880.1313-0.0973-0.13160.02920.1624-0.0085-0.00450.1174-0.02960.0135-10.2730-16.1850-62.2290
40.9810-0.01010.62290.66150.02582.91180.05140.0177-0.15570.06620.0082-0.10090.39620.0945-0.05970.19950.02210.00890.0405-0.00480.04497.7400-25.4060-46.7960
52.0860-0.07700.06342.73831.12853.10630.0624-0.6419-0.19880.7950-0.0004-0.20660.60320.1036-0.06200.4630-0.0058-0.06930.24410.05170.062510.9640-20.9390-17.4330
67.9838-1.05131.88802.46330.11972.96360.1575-0.2411-0.41610.2186-0.00160.02710.38540.1446-0.15590.27750.0125-0.02220.06910.01990.02625.7000-27.6800-31.9420
72.33220.61840.50903.78473.10824.12760.08040.14470.1228-0.13050.1379-0.3442-0.23320.4492-0.21830.21460.00140.00620.12130.00600.049112.4900-9.9020-36.1630
81.0131-0.4961-0.55301.23763.06578.2730-0.0072-0.09860.1490-0.2076-0.08220.0163-0.6042-0.20250.08940.2120-0.01820.00700.1421-0.08780.1062-9.15103.9660-27.9880
92.8570-0.37880.14851.64970.78561.49520.0108-0.09430.1976-0.0391-0.00690.0711-0.1671-0.0064-0.00380.2261-0.03120.01170.1049-0.03500.03044.25704.6610-21.5880
103.94320.2917-0.19674.2471-1.34426.4124-0.01650.33310.06000.0765-0.0498-0.3523-0.29760.49740.06630.2015-0.0327-0.00500.1673-0.04620.061321.45403.0050-15.7460
115.67440.39511.14901.14890.49052.58140.1020-0.3306-0.53570.2627-0.08270.06020.3479-0.3512-0.01930.3040-0.04790.01830.1730-0.01200.06887.2570-1.8830-3.1410
122.07580.12100.56850.95330.24043.11370.0666-0.0560-0.1805-0.0079-0.24320.30820.3094-0.53150.17660.2093-0.05750.01850.2274-0.08330.1457-16.2670-14.0800-35.3410
134.5015-3.84040.65593.3240-0.21714.5580-0.01340.0231-0.30070.0995-0.11710.30240.4581-0.61840.13040.2891-0.15640.07020.2448-0.08560.0973-14.1520-14.9430-25.1390
140.53290.6978-0.50662.38680.53144.19640.0362-0.05580.1676-0.0975-0.07030.1466-0.3813-0.13380.03400.21470.01000.00590.1447-0.07180.1560-5.1640-1.1940-35.0630
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A2A521
2A53A1022
3A103A1953
4A196A2554
5A256A3365
6A337A3536
7A354A3827
8B1B308
9B31B909
10B91B12710
11B128B22011
12B221B33612
13B337B35213
14B353B38214

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