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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 / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHoegl, A. / Sieber, S.A. / Schneider, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council725085 Germany
German Research FoundationEXC 114 Germany
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.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 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 1
B: Alanine racemase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,15329
Polymers90,5722
Non-polymers2,58227
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-346 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
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-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 381 / Label seq-ID: 24 - 403

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alanine racemase 1 /


Mass: 45285.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→84.78 Å / Num. obs: 51458 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.2 / Net I/σ(I): 6
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4390 / CC1/2: 0.85 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A3Q

4a3q


Resolution: 2.15→84.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.272 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25386 2538 5 %RANDOM
Rwork0.21685 ---
obs0.21871 48216 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 33.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å20 Å2
2--1.12 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 2.15→84.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 138 297 6435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196273
X-RAY DIFFRACTIONr_bond_other_d0.0020.025774
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9738526
X-RAY DIFFRACTIONr_angle_other_deg0.94313426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49224.91279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.904151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6481528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021183
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_other2.161.3723071
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
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 177 -
Rwork0.531 3359 -
obs--93.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1362-0.0656-0.20460.34230.90753.3664-0.0270.07130.0618-0.03710.0973-0.0906-0.07280.2821-0.07030.1880.0014-0.00390.0693-0.00440.063712.653-15.356-46.195
22.84710.28050.13971.80270.34261.9240.004-0.0360.2352-0.082-0.0799-0.1033-0.16140.09180.07590.1931-0.0065-0.00550.02830.00690.03272.199-5.986-54.724
32.7448-0.91950.77664.176-0.26482.2477-0.058-0.00960.02490.02110.02880.1313-0.0973-0.13160.02920.1624-0.0085-0.00450.1174-0.02960.0135-10.273-16.185-62.229
40.981-0.01010.62290.66150.02582.91180.05140.0177-0.15570.06620.0082-0.10090.39620.0945-0.05970.19950.02210.00890.0405-0.00480.04497.74-25.406-46.796
52.086-0.0770.06342.73831.12853.10630.0624-0.6419-0.19880.795-0.0004-0.20660.60320.1036-0.0620.463-0.0058-0.06930.24410.05170.062510.964-20.939-17.433
67.9838-1.05131.8882.46330.11972.96360.1575-0.2411-0.41610.2186-0.00160.02710.38540.1446-0.15590.27750.0125-0.02220.06910.01990.02625.7-27.68-31.942
72.33220.61840.5093.78473.10824.12760.08040.14470.1228-0.13050.1379-0.3442-0.23320.4492-0.21830.21460.00140.00620.12130.0060.049112.49-9.902-36.163
81.0131-0.4961-0.5531.23763.06578.273-0.0072-0.09860.149-0.2076-0.08220.0163-0.6042-0.20250.08940.212-0.01820.0070.1421-0.08780.1062-9.1513.966-27.988
92.857-0.37880.14851.64970.78561.49520.0108-0.09430.1976-0.0391-0.00690.0711-0.1671-0.0064-0.00380.2261-0.03120.01170.1049-0.0350.03044.2574.661-21.588
103.94320.2917-0.19674.2471-1.34426.4124-0.01650.33310.060.0765-0.0498-0.3523-0.29760.49740.06630.2015-0.0327-0.0050.1673-0.04620.061321.4543.005-15.746
115.67440.39511.1491.14890.49052.58140.102-0.3306-0.53570.2627-0.08270.06020.3479-0.3512-0.01930.304-0.04790.01830.173-0.0120.06887.257-1.883-3.141
122.07580.1210.56850.95330.24043.11370.0666-0.056-0.1805-0.0079-0.24320.30820.3094-0.53150.17660.2093-0.05750.01850.2274-0.08330.1457-16.267-14.08-35.341
134.5015-3.84040.65593.324-0.21714.558-0.01340.0231-0.30070.0995-0.11710.30240.4581-0.61840.13040.2891-0.15640.07020.2448-0.08560.0973-14.152-14.943-25.139
140.53290.6978-0.50662.38680.53144.19640.0362-0.05580.1676-0.0975-0.07030.1466-0.3813-0.13380.0340.21470.010.00590.1447-0.07180.156-5.164-1.194-35.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 52
2X-RAY DIFFRACTION2A53 - 102
3X-RAY DIFFRACTION3A103 - 195
4X-RAY DIFFRACTION4A196 - 255
5X-RAY DIFFRACTION5A256 - 336
6X-RAY DIFFRACTION6A337 - 353
7X-RAY DIFFRACTION7A354 - 382
8X-RAY DIFFRACTION8B1 - 30
9X-RAY DIFFRACTION9B31 - 90
10X-RAY DIFFRACTION10B91 - 127
11X-RAY DIFFRACTION11B128 - 220
12X-RAY DIFFRACTION12B221 - 336
13X-RAY DIFFRACTION13B337 - 352
14X-RAY DIFFRACTION14B353 - 382

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