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- PDB-6g59: Structure of the alanine racemase from Staphylococcus aureus in c... -

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Basic information

Entry
Database: PDB / ID: 6g59
TitleStructure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- 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 / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / 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
Chem-EM2 / Alanine racemase 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 / 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 / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)91,82516
Polymers90,5722
Non-polymers1,25414
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-174 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.924, 106.855, 131.023
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: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -1 - 381 / Label seq-ID: 21 - 403

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 subsp. aureus Mu50 (bacteria)
Gene: alr1, alr, SAV2070 / Production host: Escherichia coli (E. coli) / References: UniProt: P63479, alanine racemase

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-EM2 / (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate


Mass: 257.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M Hepes pH7, 2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.45→49.5 Å / Num. obs: 44955 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.6
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4399 / CC1/2: 0.5 / % 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: 2.45→49.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.869 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21489 2247 5 %RANDOM
Rwork0.19259 ---
obs0.1937 42708 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 35.447 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å20 Å2
2--1.2 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.45→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 68 171 6307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196284
X-RAY DIFFRACTIONr_bond_other_d0.0020.025811
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9648534
X-RAY DIFFRACTIONr_angle_other_deg0.939313508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74324.857280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7761528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
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_it1.6692.1123115
X-RAY DIFFRACTIONr_mcbond_other1.6622.1113114
X-RAY DIFFRACTIONr_mcangle_it2.7923.1623900
X-RAY DIFFRACTIONr_mcangle_other2.7943.1623901
X-RAY DIFFRACTIONr_scbond_it2.2622.3263169
X-RAY DIFFRACTIONr_scbond_other2.0232.2893146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.323.3454597
X-RAY DIFFRACTIONr_long_range_B_refined6.03124.286639
X-RAY DIFFRACTIONr_long_range_B_other6.02224.2366618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23844 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 161 -
Rwork0.32 3081 -
obs--99.14 %
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)
10.99850.44110.49961.18690.53991.12620.01920.0594-0.0542-0.06230.0091-0.03380.00740.0563-0.02840.15480.02420.01740.0173-0.00370.00639.5468.10435.187
21.31550.36630.43061.1530.43171.00390.027-0.0422-0.13650.0014-0.01810.02860.1173-0.0393-0.00880.13350.01980.01210.02370.01410.02412.94211.13760.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 382
2X-RAY DIFFRACTION2B-1 - 382

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