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- PDB-6g58: Structure of the alanine racemase from Staphylococcus aureus in c... -

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Basic information

Entry
Database: PDB / ID: 6g58
TitleStructure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative
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
ACETATE ION / Chem-EOW / Alanine racemase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 ...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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,79727
Polymers90,5722
Non-polymers2,22625
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-183 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.543, 106.767, 130.835
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: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 382 / Label seq-ID: 23 - 404

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

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Components

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Protein , 1 types, 2 molecules AB

#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 (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: alr1, alr, SAV2070 / Production host: Escherichia coli (E. coli) / References: UniProt: P63479, alanine racemase

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Non-polymers , 8 types, 507 molecules

#2: Chemical ChemComp-EOW / (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate


Mass: 271.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14NO5P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M Sodium acetate pH 4, 10 %(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→49.4 Å / Num. obs: 95389 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8791 / CC1/2: 0.45 / % possible all: 92

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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: 1.9→49.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.279 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16971 4787 5 %RANDOM
Rwork0.15133 ---
obs0.15224 90599 99.11 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 34.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.27 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 145 482 6647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196368
X-RAY DIFFRACTIONr_bond_other_d0.0020.025993
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9738656
X-RAY DIFFRACTIONr_angle_other_deg0.933313901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31524.7283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.828151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.481531
X-RAY DIFFRACTIONr_chiral_restr0.090.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027025
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021224
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_it1.7321.8083110
X-RAY DIFFRACTIONr_mcbond_other1.6521.8013103
X-RAY DIFFRACTIONr_mcangle_it2.4512.693892
X-RAY DIFFRACTIONr_mcangle_other2.4542.6913893
X-RAY DIFFRACTIONr_scbond_it3.2342.2653258
X-RAY DIFFRACTIONr_scbond_other3.2322.2643258
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9063.2484755
X-RAY DIFFRACTIONr_long_range_B_refined6.80823.1387105
X-RAY DIFFRACTIONr_long_range_B_other6.80923.1377105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24958 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.891→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 333 -
Rwork0.344 5966 -
obs--89.42 %
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)
11.23690.93861.42941.22161.5453.7782-0.11140.17610.1465-0.31030.00640.1311-0.38970.12570.10490.15380.0557-0.02810.0971-0.00310.03369.73716.00531.302
22.45440.82370.21312.57360.29922.81650.00910.02190.0693-0.0013-0.14660.3379-0.1376-0.29150.13750.09560.0677-0.05250.0989-0.06770.0853-5.55810.1333.77
33.7627-0.5574-0.53782.45811.04072.6313-0.0423-0.0806-0.17980.1142-0.10790.3170.3013-0.22560.15020.17190.0019-0.04930.114-0.06520.0975-7.162-6.05627.012
41.90430.90091.26591.58481.37322.3910.01250.367-0.0937-0.2020.1258-0.107-0.03570.4396-0.13830.1290.05190.00550.1576-0.02830.0115.046.70727.143
51.835-0.1590.69172.22330.02783.2974-0.03520.08420.14270.04740.1096-0.4444-0.11710.7598-0.07440.04870.0109-0.00470.2367-0.05170.105731.65814.5450.409
65.09544.90770.19937.2171-1.7794.6399-0.20660.1923-0.344-0.46620.1933-0.53360.38130.53290.01340.11750.04740.02880.2727-0.12870.117125.595.32638.13
71.1613-0.05690.38083.19091.38824.225-0.1220.17620.1944-0.21930.03640.2126-0.4303-0.07320.08560.09370.0008-0.04210.12770.02440.081112.25119.28441.814
82.7031.17153.53730.95292.1158.8272-0.0418-0.2949-0.0082-0.0019-0.08770.1742-0.1348-0.64320.12950.0909-0.00280.02340.09080.01010.08671.3458.0362.908
91.80670.13080.1041.37310.08231.52570.0516-0.08950.05330.0661-0.06150.08910.0053-0.13060.00990.01690.014-00.0605-0.02570.01749.29320.70163.722
106.8033-0.2470.38373.2197-0.96523.5119-0.12680.05910.7637-0.1301-0.00850.0172-0.40760.01650.13530.10110.0094-0.04110.0373-0.01210.100319.1636.08160.757
111.51440.37370.20092.8403-0.44011.25240.0095-0.14940.04790.157-0.0716-0.1060.04070.10460.06210.04380.0123-0.0170.0976-0.01490.014926.5222.24672.585
121.4358-0.13310.70931.10890.32022.91450.20280.0306-0.36440.0081-0.11350.18790.7148-0.2037-0.08930.233-0.0267-0.04810.0454-0.0140.14697.18-7.71151.299
135.69434.0996-0.59456.29970.63464.48810.2282-0.2812-0.53320.1173-0.2057-0.14380.52580.3175-0.02250.18550.0444-0.08730.06430.0160.121115.137-5.18557.583
144.9335-1.59211.37021.02510.21892.63920.0131-0.0885-0.05590.0138-0.09220.1513-0.0284-0.26470.07920.1126-0.01120.01020.0768-0.03640.09821.7168.40154.116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 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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